The State of Coral Reef Ecosystems of the Florida Keys

161Florida Keys

1. NOAA, Florida Keys National Marine Sanctuary

2. Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute

3. Reef Environmental Education Foundation 9. NOAA, Office of National Marine Sanctuaries

4. University of Miami, Rosenstiel School for Marine and Atmospheric Science 10. NOAA, National Ocean Service, Special Projects Office

5. NOAA, Southeast Fisheries Science Center 11. Scripps Institute of Oceanography

6. Florida International University, Southeast Environmental Research Center 12. University of North Carolina, Wilmington

7. Florida Department of Environmental Protection 13. Mote Marine Laboratory

8. Monroe County Division of Marine Resources 14. U.S. Environmental Protection Agency, Gulf Ecology Division9. 

The State of Coral Reef Ecosystems of the Florida Keys

Scott Donahue1, Alejandro Acosta2, Lad Akins3, Jerald Ault4, James Bohnsack5, Joseph Boyer6, Michael Callahan2, 

Billy Causey1,9, Carrollyn Cox2

, Joanne Delaney1, Gabriel Delgado2, Kent Edwards1,7, George Garrett8, Brian Keller9, G. Todd Kellison5, 

V. Robert Leeworthy10, Lauri MacLaughlin1

, Loren McClenachan11, Margaret W. Miller5, Steven L. Miller12, Kim Ritchie13, 

Steven Rohmann10, Deborah Santavy14, Christy Pattengill-Semmens3

, Benjamin Sniffen1, Stephen Werndli1 and Dana E. Williams5

Introduction and Setting

In this chapter, the authors present the latest in a series of updates to this living document. The 2005 edition of this report provided a good basis for this update, as it nicely detailed the coral reefs of the Florida Keys and southeast Florida, 

along with their associated oceanography, reef geomorphology and geology, and socioeconomic importance (Andrews et 

al., 2005). This edition of the report provides two separate chapters for the coral reefs of Florida in appreciation of their 

separate regulatory histories and the different reef types present in the Florida Keys and the Southeast region. The two 

chapters will complement each other and should be used to highlight the challenges associated with managing a coral 

reef ecosystem that extends over 480 km (300 miles). Contributing authors for the Florida chapter in Waddell (2005) 

were contacted for this chapter and only those updates available at the time of this writing were included. Manuscripts 

and information that were in preparation will be included in the next edition of this volume. Figure 6.1 highlights locations 

mentioned throughout this chapter. 

!H

!H

!H

!H

81°W

81°W

83°W

83°W

26°N26°N

24°N24°N

Aguijan Tinian

0 20 40 km

!H City

Florida Keys National

Marine Sanctuary

National Park (NP)

National Wildlife Refuge (NWR)

State Park

Ecological Reserve

Land

Water <20 m

Deep Water

EEZ

Big Cypress

National Park

B R O W A R D

C O L L I E R

M O N R O E

M I A M I - D A D E

Everglades National Park

Biscayne

 NP

Dry Tortugas

National Park

Tortugas

Ecological

Reserve

Tortugas

Ecological

Reserve

Western

Sambo

Ecological

Reserve

L E E

H E N D R Y

P A L M B E A C H

Ten Thousand

Islands NWR

Whitewater Bay

Crocodile

Lake NWR

Key Deer

Great White NWR

Heron NWR

Key West NWR

Marquesas Keys

Key

West

Marathon

Looe Key

Florida Bay

Mosquito Bank

John Pennekamp Coral Reef

State Park

South

Carysfort

Miami

Everglades City

Figure 6.1. Locator map of the Florida Keys depicting locations mentioned in this chapter. Map: K. Buja. 
The State of Coral Reef Ecosystems of the Florida Keys

162Florida Keys

Environmental and anthropogenic stressors

Climate Change and Coral Bleaching 

Although elevated sea surface temperatures (>31°C) returned to the Florida Keys in 2004 and 2005, only minor to moderate coral bleaching was observed in patchy patterns on the coral reefs. While severe coral bleaching events were 

observed and recorded in other parts of the U.S. Caribbean, the Florida Keys escaped most of the stressful environmental conditions experienced elsewhere. Due to an active hurricane season both in 2004 and 2005, extended periods 

of doldrum-like weather patterns did not establish in the Florida Keys. The passage of each tropical storm or hurricane 

decreased sea surface temperatures, as well as allowing for mixing of the surface waters due to intense winds. 

Figure 6.2 shows how the waters cooled off 

just after the passage of three hurricanes in 

the Florida Keys in 2005. Illustrated are the 

2004 and 2005 sea surface temperatures 

that were recorded at a SeaKeys C-Man 

station established at Sombrero Reef located on the reef tract off the middle Florida 

Keys. In 2005, elevated sea surface temperatures (>31oC) were present between July 

and September 2005. Doldrum-like weather 

patterns persisted for most of the time and 

corals began to bleach and show signs of 

stress. Before a mass bleaching event occurred, the passage of Hurricanes Katrina, 

Rita and Wilma alleviated the stressful conditions of elevated sea surface temperatures and doldrum weather patterns. More 

information on the effects of bleaching on 

reefs in the Florida Keys can be found in the 

Benthic Habitats section of this chapter.

Diseases 

Corals throughout the Caribbean and Atlantic region have suffered from numerous diseases over the past several decades, and disease has been implicated in the demise of a number of reef building species. Two studies in the Florida 

Keys track disease prevalence at monitoring stations throughout the archipelago. In one study, the prevalence of diseases has been shown to vacillate over time, and since 2002 has generally decreased at monitored stations within Florida 

Keys National Marine Sanctuary (FKNMS) and at the Dry Tortugas. Because diseases can be difficult to distinguish in 

the field, this study grouped white diseases (white plague, white pox, white band) to differentiate them from black band 

disease, while the remainder of disease states fell into an “Other” category. The number of stations affected with white 

diseases peaked to more than 80% in 2002, subsided to 35% in 2005, then increased again to 50% in 2006. The number 

of stations affected with Other diseases peaked to 90% in 2001, but declined to 57% by 2006. The other reported study, 

which was conducted in August of 2006, focused on diseases affecting two species of coral that had been recently listed 

as threatened on the U.S. Endangered Species List: Acropora cervicornis and A. palmata. The group surveyed 107 sites 

along about 46 km of coastline in the upper keys and fortunately found no evidence of white band or other diseases affecting either species. More information on the effects of coral diseases on reefs in the Florida Keys can be found in the 

Benthic Habitats section of this chapter.

Tropical Storms

Tropical cyclones are an annual threat to Florida coastal ecosystems and may impose a variety of devastating effects, 

including storm surge, freshwater flooding due to excessive rainfall and damaging winds. The 2005 hurricane season had 

very serious impacts to Florida coastal resources, whereas the 2006 and 2007 seasons produced more minor, localized 

impacts (Figure 6.3). The record-breaking 2005 Atlantic Hurricane Season produced a total of 28 named tropical storms, 

15 of which attained hurricane strength throughout the Atlantic, Caribbean Sea and Gulf of Mexico. Of these storms, five 

tropical cyclones directly impacted the Florida Keys, with a frequency of one storm per month. Tropical Cyclone Arlene, 

the first one to affect Florida Keys in 2005, passed west of Dry Tortugas before making landfall west of Pensacola in early 

June. Hurricane Dennis passed over Dry Tortugas approximately one month later, causing severe erosion from west of 

John Pennekamp State Park through the Dry Tortugas. Compared with the other tropical cyclones to affect the Florida 

Keys in 2004 and 2005, Dennis was noted by FKNMS resource managers for its powerful hydrodynamic energy. Approximately a month and a half later, Hurricane Katrina struck south Florida as a Category 1 hurricane in late August. Only 

minor wind and storm surge damage was reported throughout mainland south Florida, however, rainfall in excess of 10 

inches produced major freshwater flooding southwest of Miami and throughout the Lower Florida Keys. As Katrina passed 

over the Dry Tortugas, only minor overwash of the sand beaches and docks was reported. Hurricane Rita passed south of 

the Florida Keys in late September. While minor wind damage and no freshwater flooding was reported, significant storm 

surge flooding in excess of 5 ft above normal was reported along Atlantic-facing shores of the Keys, producing wideFigure 6.2. Sea surface temperatures (SST) recorded at Sombrero Reef in the 

Florida Keys between January 2004 and December 2005. Passage of hurricanes 

Katrina, Rita and Wilma in September and October 2005 alleviated the stressful 

conditions of elevated sea surface temperatures and doldrum weather patterns.

DHW=Degree Heating Weeks. Source: NOAA/ NESDIS.
The State of Coral Reef Ecosystems of the Florida Keys

163Florida Keys

spread overwash of sand beaches. The last 

tropical cyclone to affect Florida in 2005 was 

Hurricane Wilma, which was the most devastating to the Florida Keys. Wilma struck 

the coastline of extreme southwest Florida, 

south of Everglades City, in late October as 

a major hurricane. Widespread storm surge 

reached 8 ft above normal and completely 

overwashed most of Florida Keys from Marathon westward, with storm surge likely in 

excess of 8 ft across the Everglades coastline south of Everglades City. Severe wind 

damage was also noted in the Key West 

National Wildlife Refuge in the Marquesas 

Keys, with numerous mangrove branches 

snapped and some plants completely uprooted. While damage to mangrove forests 

resulted in some displacement of local bird 

populations, sand deposition on beaches 

may have benefited turtles nesting in the 

Keys. The 2006 hurricane season included 

two landfalls in Florida: Tropical Storm Alberto along the Big Bend coastline in June, and 

Hurricane Ernesto (which soon weakened to 

tropical storm intensity) which swept across 

the Florida Keys and southwest Florida in 

August. Ernesto did not produce significant 

coastal erosion in the Florida Keys.

Damage and destruction resulting from tropical cyclones are usually thought of in terms of land-based observations. 

However, the marine ecosystem is always affected by these storms as well. Many marine habitats surveyed in the Dry 

Tortugas region suffered obvious physical damage (e.g., overturned coral colonies) and scouring from the storms that hit 

the region in 2005. Many areas that were gorgonian-dominated hard-bottom habitats in 1999-2000 and 2002, especially 

in the southern portion of Dry Tortugas National Park (DTNP), are now devoid of most gorgonians and sponges. Interestingly, concurrent reef fish surveys documented a marked decline in the abundance of juveniles of some species (e.g., 

black grouper) that were previously relatively abundant in these habitats. Reef terraces on Little Tortugas Bank and the 

northwestern Tortugas Bank (Sherwood Forest) are still in relatively good condition in terms of coral abundance, but coral 

cover has apparently declined from about 50% to about 35% in some areas. In these same sites, scientists noticed an 

increased prevalence of the brown alga Lobophora variegata that now occupies space once covered by live coral. A few 

sites also exhibited relatively high prevalence of coral disease, especially by what is believed to be white plague. At one 

site in particular, approximately 25% of the corals were afflicted with this condition. The factors responsible for increasing disease prevalence are unknown. The hypothesis that coral bleaching and other stressors increase susceptibility to 

disease needs to be tested. However, the extent, severity and degree of recovery from coral bleaching that occurred in 

2005 are unknown.

Relative to 1999-2000, June 2006 sampling efforts revealed that sea urchins, especially Diadema antillarum, were more 

abundant and were found in relatively dense aggregations (>0.3 individuals/m2) in some of the shallow water patch reef, 

hardbottom and medium-profile reef areas in DTNP (Miller et al., 2006a). While Diadema densities are still below the 

estimated historical (pre-1983) densities (approximately 1 individual/m2 for certain habitat types), urchin densities in the 

Tortugas region, especially within DTNP, remain about an order of magnitude higher than levels documented in the rest 

of the Florida Keys. An increase in the number of recently recruited juvenile Diadema in the region is encouraging; peak 

recruitment in south Florida normally occurs during August and September. Of the 98 Diadema recorded at 46 monitoring sites, about 75% measured less than 1 cm in test diameter and were believed to have settled in the previous two 

months.

Coastal Development and Runoff

A major influence on water quality in Florida Bay and the Keys is runoff from south Florida and the Everglades. In the 

later third of the 20th century, it was recognized that modifications to drainage of fresh water in the south Florida region 

resulted in serious environmental effects. The drainage system, known as the Central and Southern Florida Project 

(C&SF), was constructed by the U.S. Army Corps of Engineers (USACE) and was the focal point of the south Florida 

water management system for the past 50 years. The Water Resource Development Acts of 1992 and 1996 provided the 

USACE with the authority to review the C&SF, and to develop a comprehensive plan to restore and preserve the south 

Florida ecosystem by enhancing fresh water flow into the Everglades while maintaining flood protection in the surrounding 

areas. In April 1999, the Comprehensive Everglades Restoration Plan (CERP) was finalized, which detailed more than 60 

Figure 6.3. The paths and intensities of tropical storms affecting the Florida Keys, 

2000-2007. Storm name, year and strength are indicated for each. Map: K. Buja. 

Source: http://maps.csc.noaa.gov/hurricanes/.

LILI (2002) H2 LILI (2002) H2

FRANCES (2004) H2

JEANNE (2004) H3 JEANNE (2004) H3

WILMA (2005) H2 WILMA (2005) H2

RITA (2005) H2 RITA (2005) H2

WILMA (2005) H3 WILMA (2005) H3

DENNIS (2005) H1 DENNIS (2005) H1

MICHELLE (2001) H1 MICHELLE (2001) H1

KATRINA (2005) H1 KATRINA (2005) H1

DENNIS (2005) H4 DENNIS (2005) H4

KATRINA (2005) H3 KATRINA (2005) H3

CHARLEY (2004) H4 CHARLEY (2004) H4 CHARLEY (2004) H1 CHARLEY (2004) H1

RITA (2005) H1 RITA (2005) H1

RITA (2005) H3

IVAN (2004) H4 IVAN (2004) H4

DENNIS (2005) H3 DENNIS (2005) H3

RITA (2005) H4 RITA (2005) H4

DENNIS (2005) H2 DENNIS (2005) H2

JEANNE (2004) H2 JEANNE (2004) H2

WILMA (2005) H3 WILMA (2005) H3 WILMA (2005) H2 WILMA (2005) H2

DENNIS (2005) H3 DENNIS (2005) H3

80°W

80°W

25°N25°N

Category

1

2

3

4

5

0 50 100 km

Hurricanes

2000-2007

GORDON (2000) H1 GORDON (2000) H1
The State of Coral Reef Ecosystems of the Florida Keys

164Florida Keys

major changes to fresh water delivery that needed to occur in and around the Florida Everglades. If implemented, these 

changes will affect an area of more than 18,000 square miles. More information on CERP can be found at http://www.

evergladesplan.org/index.aspx. 

Coastal development also affects nearshore water quality in the Florida Keys, and as a result, Monroe County has developed Master Stormwater and Wastewater Plans (MSWWW) designed to comprehensively address the significant local 

sources of pollution in Florida Keys waters. Construction has been completed on some of the MSWWW projects and several others have been initiated. Additionally, the state of Florida has mandated that all homes and businesses in Monroe 

county be hooked up to centralized sewage treatment plants (the wastewater portion of the MSWWW) by the year 2010, 

thus the county government is actively seeking funding from several sources to meet this aggressive schedule. There are 

also several local, state and federal regulatory programs in place that were designed to reduce and mitigate the impacts 

of upland development on natural habitats and coastal water quality. More information about these programs can be 

found on the Internet for Monroe County (Rate of Growth Ordinance, Section 9.5-120 Monroe County Code http://www.

municode.com/resources/gateway.asp?sid=9&pid=11270) and state and federal wetlands and surface water (http://www.

dep.state.fl.us/water/wetlands/erp/index.htm). 

In an effort to keep the beach-going public informed about water-borne microorganisms that could cause disease, infections or rashes, the Florida Department of Health monitors water quality at a number of beaches in 34 coastal counties. 

Monroe County has 17 beaches that are tested weekly for Enterococci and fecal coliform bacteria. High concentrations of 

these bacteria prompts the issuance of health advisories or warnings for that week. There were 884 beach weeks tested 

in Monroe County in 2006 (17 beaches x 52 weeks), ninety of the tests (about 10%) resulted in advisories and warnings. 

Additional information about beach water quality for the Florida Keys can also be found at http://esetappsdoh.doh.state.

fl.us/irm00beachwater/default.aspx?county=Monroe. 

Coastal Pollution 

In addition to the information presented in the Costal Development and Runoff section above, please refer to the Southeast Florida chapter of the 2005 edition of this report (Andrews et al., 2005) for further information. 

Tourism and Recreation

Artificial reefs have previously been deployed in the Florida Keys (e.g., at Adolphus Busch, Thunderbolt, Duane, etc.). In 

2000-2001, Johns et al. (2001) estimated that both residents and visitors of the Florida Keys spent 1.58 million persondays snorkeling, SCUBA diving and fishing on the artificial reefs in the FKNMS. This activity generated over $131 million 

in output/sales, $31 million in income, and 2,365 full and part-time jobs in Monroe County. In addition, the artificial reefs 

had an estimated net annual user value of $9.75 million with an asset value of $57.5 million. Residents and visitors were 

willing to pay annually an additional $2 million for new artificial reefs.

The FKNMS currently has a moratorium on deployment of additional artificial reefs, with the exception of the USS Vandenberg, which was given approval by National Oceanic and Atmospheric Administration (NOAA) and FKNMS in 2003 

and is scheduled to be placed in mid-2008. The moratorium was enacted because of concerns about whether artificial 

reefs will harm or help the natural reefs in the FKNMS.

In June 2002, the retired navy ship USS Spiegel Grove was sunk in the waters off Key Largo in the FKNMS. At 510 ft, the 

Spiegel Grove was at the time the largest vessel ever intentionally sunk for the purpose of creating an artificial reef within 

the FKNMS. Proponents of the Spiegel Grove argued that the ship’s role as an artificial reef would take pressure off the 

surrounding natural reefs and thus provide an ecological benefit. Leeworthy et al. (2006) tested this hypothesis over a 10-

month period via a pre- and post-sinking monitoring effort. A combination of dive shop logbooks and on-water observation 

were used to estimate total use on the artificial and natural reefs surrounding the area where the Spiegel Grove was to 

be sunk. The study found that after the sinking of the Spiegel Grove, usage of surrounding natural reefs declined 13.7%, 

while use of artificial reefs increased 160.5% and total reef use (artificial and natural) increased 9.3%. In addition, dive 

shop business increased 3.7% and total recreation and tourism increased as well, resulting in an additional $2.7 million in 

total sales/output, $962,000 in income and 68 full and part-time jobs in the Monroe County economy. 

Additional visitor and resident surveys to 

track the use of Florida Keys reefs and associated economic benefits are scheduled 

to be conducted in 2008 and summary results and reports are expected to be available according to the schedule in Table 6.1. 

More detailed analysis of the data, which 

requires more time to analyze, review and 

publish, will be included in future versions of 

this report as it becomes available. 

AVAILABLE REPORT

April 15, 2009 Visitor Profiles Report

May 15, 2009 Visitor Economic Contribution Report

June 15, 2009 Visitor Importance - Satisfaction Ratings Report

June 15, 2009 Resident Survey Report: Profiles, Economic Contribution and 

Importance-Satisfaction Ratings

July/August 

2009

Visitor and Resident Survey: Knowledge, Attitudes and Perceptions of Sanctuary Management Strategies and Regulations

Table 6.1. Schedule of completion for the Florida Keys Visitor Survey reports. 

Source: V.R. Leeworthy.
The State of Coral Reef Ecosystems of the Florida Keys

165Florida Keys

Knowledge, Attitudes and Perceptions of Regulations and Management Strategies in the FKNMS

In 2005, NOAA funded replication of a baseline study completed in 1995-1996 by researchers at the University of Florida 

and the University of Miami’s Rosenstiel School of Marine and Atmospheric Sciences through a Florida Sea Grant Project. 

Baseline information was obtained on the knowledge, attitudes and perceptions about regulations and management strategies being proposed for the FKNMS and the no-take areas established in 1997. The baseline and 10-year replication 

will assess changes in the knowledge, attitudes and perceptions of FKNMS regulations and management strategies for 

three user groups: commercial fishermen, dive shop owners and operators and members of local environmental groups. 

Surveys of commercial fishermen and dive shop owners/operators were completed in 2006. A 100% response rate was 

achieved on a random sample of 300 commercial fishing operations, and a 95% response rate was achieved for all 65 

dive shop owners/operators in the Florida Keys in 2006. The survey of members of local environmental groups began in 

December 2006 and was completed in May 2007. Analyses and reports are expected to be available by 2008. For more 

information about ongoing socioeconomic research, visit http://marineeconomics.noaa.gov/welcome.html.

Fishing

Both recreational and commercial fishing occur regularly in Florida Keys waters. From a recreational standpoint, fishers 

are either local residents (roughly one third of Florida’s total population of approximately 18 million people live in Southeast Florida or the Keys) or non-residents visiting “The Fishing Capitol of the World,” as the state of Florida promotes itself 

(Ault et al., 2005a; FWC, 2007). 

Total fishing activity in the Florida Keys reflects Florida’s increasing population, which 

grew tenfold from 1930 to 2007 (Ault et al., 

2005b). Recreational vessel registrations in 

Monroe County increased more than 1000% 

from 1964 to 2006, while commercial vessel 

registrations increased by about 100% from 

1964 to 1998 but have since decreased by 

37% (Bohnsack, et al., 1994; Figure 6.4). 

Precise data on fishing effort on coral reefs 

do not exist, but are reflected by statewide 

and regional fishing statistics. In the five 

most recent years for which recreational 

fishery estimates are available (2001-2005) 

for Florida, more than 6.4 million anglers averaged 27.2 million marine fishing trips annually. An estimated 173.3 million fish were 

caught annually, of which slightly more than 

50% were released (86.9 million; NMFS, 

2007). Two recent (2000-2001, 2003) nonconcurrent studies showed that 3.64 million 

person days were spent fishing on natural 

reefs annually in the Florida Keys (Johns et 

al., 2001; Johns et al., 2004). Concomitant 

with increasing fishing pressure associated with increasing population, average fishing power (the proportion of stock 

removed per unit of fishing effort) may have quadrupled in recent decades because of technological advances in fishing 

tackle, hydroacoustics (depth sounders and fish finders), navigation (charts and global positioning systems), communications and vessel propulsion (Bohnsack and Ault, 1996; Mace, 1997). 

Fishing can stress coral reefs by removing targeted species and by killing nontarget species as bycatch, both of which 

may result in cascading ecological effects (Frank et al., 2005). Because fishing is size-selective, concerns exist about 

ecosystem disruption by removal of ecologically important keystone species, top predators (e.g., groupers, snappers, 

sharks and jacks), and prey (e.g., shrimps and baitfish). 

Fishing can also negatively impact reef ecosystems via fishing-related habitat damage. Commercial fisheries for lobsters 

and stone crabs in the Keys utilize traps that are deployed in habitats adjacent to reefs. Strong storms can move traps 

onto reefs, where corals and other benthic organisms are damaged or killed (e.g., Sheridan et al., 2005). In 2005, approximately 300,000 lobster traps were believed to have been lost during a series of hurricanes and strong storms (Clark, 

2006). Many reefs throughout the Keys are littered with lost traps and with monofilament line lost by recreational anglers. 

Reef damage may also occur from anglers anchoring on reefs (Davis, 1977). Finally, stress associated with fishing-related removal of species and habitat damage may be compounded when combined with other stressors such as pollution 

and climate change (Wilkenson, 1996). 

Figure 6.4. Southern Florida (Monroe, Dade, Broward, Palm Beach and Collier 

Counties commercial and recreational vessel registrations from 1964 to 2007. 

Sources: Florida Statistical Abstracts and Florida Department of Highway Safety 

and Motor Vehicles.

0

5,000

10,000

15,000

20,000

25,000

30,000

1960 1970 1980 1990 2000 2010

number of vessel Registrations

Commercial

Recreational
The State of Coral Reef Ecosystems of the Florida Keys

166Florida Keys

Trade in Coral and Live Reef Species

The trade in coral and live reef species is not considered a major direct threat to coral reef ecosystems in Florida. The 

collection and sale of living corals and hard substrate with attached organisms (“live rock”) has been prohibited in state 

waters of Florida since 1995 and in federal waters since 1997. The state and federal government both regulate a small 

but viable fishery based in live rock aquaculture, where geologically-unique limestone is placed on the ocean floor and 

acts as a recruitment site for hard and soft corals and other marine invertebrates. While the fishery remains commercial 

in nature (mature live rock is sold in the aquarium trade), opportunities to use aquacultured live rock for mitigation or 

restoration may exist in the future.

Similar to live rock aquaculture, the collection and sale of live reef species comprises a small but well-managed fishery, 

most notably in the Florida Keys. Approximately 147 endorsements (permits) were issued for the live collection of ornamental vertebrates and invertebrates for sale in the aquarium industry in Monroe County in 2007. State-wide landings in 

2005 included 147,290 total finfish and 8,611,912 individual invertebrates (e.g., polychaete worms, tunicates, crabs, sea 

stars and anemones). The fishery has been regulated by the state fisheries agency (currently the Florida Fish and Wildlife 

Conservation Commission or FWC) since 1991. Florida Keys fishermen have been exemplary in initiating regulations for 

their fishery and monitoring fluctuations in the variety of species they harvest. Concerned fishermen of the Keys continue 

to work with the FWC to suggest rule changes to ensure sustainability of the marine life fishery.

Ships, Boats and Groundings

Vessel groundings in the Florida Keys occur regularly, and each impacts the benthic environment. The significance of 

these groundings, and associated restoration alternatives, was detailed in the Florida chapter of the State of the Coral 

Reef Ecosystems of the United States and Pacific Freely Associated States: 2005 (Andrews et al., 2005). In the Florida 

Keys, the number of reported vessel groundings from years 2002 to 2006 decreased annually (721, 655, 433, 424, and 

301 respectively), but it is not possible to determine if this trend is a result of fewer boaters using the resource because of 

higher fuel costs, increased boater awareness of the sensitivity of the environment, or a decreased willingness to call for 

assistance if boaters run aground. Generally, there has been no proportional shift in impact to different habitat types with 

approximately 14% of groundings in coral habitat, an estimated 85% in seagrass and about 1% in hardbottom.

Marine Debris

Traps and “Casitas”

During the 2005 hurricane season, the Keys were subjected to several major storms which mobilized and damaged commercial lobster and stone crab traps, making it practically impossible for fishermen to locate and retrieve their fishing gear. 

Florida state law (Chapter 68B-55 FAC), which normally prohibits removal of commercial traps by anyone other than their 

owner or law enforcement officers, threatened to hinder removal efforts. Ultimately, the state of Florida partnered with 

Monroe County to recover more than 45,000 traps from Monroe County waters, at a cost of more than $1.8 million. Marine 

debris removal also occurs on a smaller scale, as community coastal cleanup events are regularly organized throughout 

the year. These events help eliminate trap-related debris that has washed onto mangrove islands and beaches. 

Casita is a term used to describe a particular type of fishing gear used to attract spiny lobsters elsewhere in the Caribbean. The term is Spanish in origin and translates as “little house.” Within the FKNMS, casitas are not considered traditional 

fishing gear, and thus are subject to regulation via the National Marine Sanctuaries Act (NMSA) and the Florida Keys National Marine Sanctuary and Protection Act (FKNMSPA). As such, it is against FKNMS regulations to place casitas inside 

FKNMS boundaries, and it is illegal to harvest spiny lobster from any artificial structure throughout the state of Florida. 

Casita placement (and presumably the associated lobster harvest) is common in the backcountry area north of the Lower 

Keys, and there is concern among wildlife management agencies that there could be detrimental effects to natural habitat 

and lobster population dynamics as a result. Additionally, there are concerns in the commercial trap fishing industry that 

this practice is unfairly shifting fishery allocation away from the legal lobster trap fishers. In July 2007, a cooperative effort 

between state and federal partners was implemented to target and remove casitas in the Lower Keys. Simultaneously, 

fisheries biologists from the state of Florida began evaluating the effect of casitas on the ecology of the backcountry area 

and the lobster fishery in response to a request from FWC Commissioners. 

Derelict and Abandoned Vessels

In a typical year, approximately 100 boats are abandoned in the Florida Keys. In addition to this number, the 2004 and 

2005 hurricane seasons caused more boats to be moved into sensitive habitats like seagrass beds and mangrove islands. After the 2005 hurricane season, Monroe County initially surveyed 355 vessels aground, but cleanup operations 

ultimately removed nearly 500 vessels from the water. More information on derelict and abandoned vessel removal programs can be found at http://myfwc.com/boating/DerelictVessels.htm. 

Aquatic Invasive Species

Non-native (exotic) fishes have been increasingly documented in Florida coral reef environments. These species have the 

potential to disrupt natural coral reef communities due to increased predation of natural species, increased competition 

for available space and potential introduction of diseases. More than 18 species of non-native marine fish have been doc-
The State of Coral Reef Ecosystems of the Florida Keys

167Florida Keys

umented from Miami/Dade, Broward and 

Palm Beach counties in Southeast Florida 

(REEF database, 2006). Lionfish (Pterois 

volitans and P. miles), which are included in 

this number, have become well established 

along the U.S. east coast, Bermuda and the 

Bahamas (Figure 6.5). The most likely pathway for introduction of these exotic species in Florida waters is aquarium releases 

(Semmens et al., 2004)

Reports of lionfish range from Rhode Island 

to the Turks and Caicos Islands, but as of 

December 2006, no sightings had been 

reported from Biscayne National Park, the 

Florida Keys or the Dry Tortugas. The northern records of lionfish sightings have been 

limited to juvenile fish, however the southern range appears to be expanding both 

spatially and in abundance. Research by 

NOAA’s National Center for Coastal Ocean 

Science, Center for Coastal Fisheries and Habitat Research shows that the thermal tolerance of P. volitans/miles (11°C 

minimum) appears to preclude their adult establishment north of North Carolina (Kimball et al., 2004)). However, the increasing abundance and distribution of lionfish in the South Atlantic Bight, Bermuda, Florida and the Bahamas provides 

strong evidence suggesting lionfish are the first marine fish species to successfully establish a breeding population in the 

tropical western Atlantic. The venomous nature of lionfish, combined with their voracious feeding habits, unique reproduction and few predators, indicate successful invasive abilities. Sightings of non-native marine fish are being tracked 

through the REEF Volunteer Fish Survey Project in partnership with federal and state agencies in the hope of preventing 

additional successful invasions in Florida’s marine waters. 

Security Training Activities

The 2004 closing of the Navy base in Vieques, Puerto Rico, has not resulted in the anticipated increase in military activities that threaten the coral reef ecosystems of the Florida Keys, but the U.S. Navy is increasing its readiness by improving 

housing, dockage and aircraft facilities in the Key West area. Plans for grading along the runways of Naval Air Station 

Key West are being developed that will improve safety conditions there. This construction will affect mangrove and marsh 

systems, but will not directly affect nearby seagrass and coral resources. In general, security training activities of the U.S. 

Navy and U.S. Coast Guard are not recognized as a major threat to coral reef ecosystems in Florida. Although these activities can change in response to threats to national security or the need to maintain readiness (e.g., illegal immigration 

from Caribbean nations), military operations usually undergo review and revision to minimize environmental impacts. 

Offshore Oil and Gas Exploration

There is currently no oil or gas drilling occurring in state waters. Florida law prohibits future leasing or drilling of the seabed within the state’s Territorial Sea for purposes of oil and gas exploration and development. Holders of any offshore 

drilling leases that were granted by the state prior to the enactment of the current law must obtain permits under state 

environmental laws and regulations prior to conducting any drilling activities. No leases exist in Florida areas where coral 

reef tracts are located.

Figure 6.5. Pterois volitans, one of two species of lionfish from the Pacific, has become established along the U.S. east coast. It was probably imported for use in an 

aquarium before being released by its owner into the wild. Photo: P. Whitfield.
The State of Coral Reef Ecosystems of the Florida Keys

168Florida Keys

CoRal REEF ECoSySTEmS—daTa-gaThERIng aCTIvITIES and RESouRCE CondITIon

Historical Ecology of the Florida Keys

Like reef communities worldwide, the Florida Keys have been degraded by overfishing and habitat loss. The roots of degradation pre-date scientific data collection, so

Figure 6.6. Time line for sources of historic resource information about the Florida 

f Keys. Source: L. McClenachan, unpub. data.

historic data are needed to assess longterm change. Historical data sources range

from logs kept by early Spanish and British explorers to fishing guides written by

recreational fishermen in the 20th century

(Figure 6.6). For example, the British cartographer, George Gauld, spent 17 years

mapping the Keys in the 1760s and kept

a journal where he described the reef as

full of fish and wrote that, “there are such

quantities of the largest [lobster], that a boat

may be loaded with them in a few hours.”

Gauld also mapped much of the coral reefs

in the Florida Keys (Figure 6.7). This kind o

historical information can help to develop a 

baseline for understanding how the natural

Figure 6.7. Gauld’s 1775, “A Plan for the Gulf of Florida”. Source: Gauld, 1775.

system functioned before human impacts.

Specific changes documented by historical ecology research include: 1) loss of top

predators, such as an extinct species of

monk seal which was historically ubiquitous

and abundant in coral reef communities; 2)

loss of spawning aggregations and reductions in numbers of large fish, such as groupers that have been intensively fished since

the 18th century; 3) loss of habitat structure

including mangroves, corals and seagrass;

4) reductions in invertebrate populations including conchs, lobsters and urchins; and

5) loss of ecosystem services, such as water filtration by sponges. For example, at its

peak, the sponge fishery in the northern Caribbean removed six million pounds of live

sponge annually (Figure 6.8). Understanding the degree of change that has occurred 

over time and how the ecosystem functioned in a more pristine state is essential 

for management and restoration of Florida’s 

ecologically and economically important 

reef communities.

A number of coral reef ecosystem monitoring 

projects are underway in the Florida Keys, 

making it one of the most intensively studied coral jurisdictions in the U.S. Although 

no summary table of monitoring activities 

or map showing the distribution of monitoring locations were prepared for this chapter, 

many of the important ongoing activities are 

described below.

Figure 6.8. Landings of live sponge in Florida, 1850-1940. At its peak, the fishery 

removed 600,000 lbs annually in dry weight, which is equivalent to approximately 6 

million lbs of live sponge. Source: McClenachan, 2008.

700,000

600,000

weight)

500,000

dry (lbs 

400,000

landed 

300,000

Sponges 

200,000

100,000

0

93715937159371593715937

4556667788899

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1
The State of Coral Reef Ecosystems of the Florida Keys

169Florida Keys

Water Quality AND OCEANOGRAPHIC CONDITIONS

Background and methods for this section are detailed in the Florida chapter of the previous report (Andrews et al., 2005) 

and the FY2006 Annual Report of the Water Quality Monitoring Project for the Florida Keys National Marine Sanctuary

(Boyer and Briceño, 2007). Only new information and related discussion are presented in this section.

Several water quality variables were measured in situ and from grab samples at 154 fixed stations within the FKNMS 

boundary from March 1995 to December 2006 (Figure 6.9). Stations were stratified according to water quality characteristics (i.e., physical, chemical and biological variables) using multivariate statistical techniques, an approach that has been 

very useful in understanding the factors influencing nutrient biogeochemistry in Florida Bay, Biscayne Bay and the Ten 

Thousand Islands (Boyer and Briceño, 2007). Data from individual sites for the complete period of record were plotted as 

time series graphs to illustrate any temporal trends that might have occurred. Temporal trends were quantified by simple 

regression with significance set at p<0.05. 

Summary statistics for water quality variables from all 46 sampling events are shown as median, minimum, maximum 

and number of samples (Table 6.2). Overall, the region was warm and euhaline with a median temperature of 27.1°C and 

salinity of 36.2; oxygen saturation of the water column (DOsat) was relatively high at 88.5%. On this coarse scale, Sanctuary waters exhibited very good water quality with median nitrate (NO3

-

), ammonium (NH4

+), and total phosphorus (TP) 

concentrations of 0.09, 0.29, and 0.19 μM, respectively. Ammonium was the dominant dissolved inorganic nitrogen (DIN) 

species in almost all of the samples (about 70%). However, DIN comprised a small fraction (4%) of the total nitrogen (TN) 

pool with total organic nitrogen (TON) making up the bulk (median 11.2 μM). Soluable reactive phosphorus (SRP) concentrations were very low (median 0.02 μM) and comprised only 6% of the TP pool. Chlorophyll a (CHLA) concentrations 

were also very low overall, 0.23 μg l-1, but ranged from 0.01 to 15.2 μg l-1. Total organic carbon (TOC) was 178.0; a value 

higher than open ocean levels but consistent with coastal areas. Median turbidity was low (0.63 nephelometric turbidity 

units or NTU) as reflected in a low light extinction coefficient or Kd value of 0.204 m-1. This resulted in a median photic 

depth (to 1% incident photosynthetically active radiation or PAR) of approximately 22 m. Molar ratios of nitrogen (N) to 

phosphorus (P) suggested a general P limitation of the water column (median TN:TP=61.6) but this must be tempered by 

the fact that much of the TN is not bioavailable.

Figure 6.9. The Southeast Environmental Research Center (SERC) Water Quality Monitoring Network showing the distribution of fixed 

sampling stations, indicated by +, within the FKNMS and Florida Bay, Biscayne Bay, Whitewater Bay, Ten Thousand Islands and Southwest Florida Shelf. SFWMD=South Florida Water Management District. Source: Boyer and Briceño, 2006.
The State of Coral Reef Ecosystems of the Florida Keys

170Florida Keys

Several important results have been realized from this monitoring project. The first 

is the documentation of elevated DIN in the 

nearshore zone of the Florida Keys (Figure 6.10). This result was evident from our 

first sampling event in 1995 and continues 

to be a characteristic of the ecosystem. Interestingly, this gradient was not observed 

in a comparison transect from the Tortugas. 

This type of distribution implies an inshore 

source which is diluted by low nutrient Atlantic Ocean waters. Presence of a similar 

gradient in TOC and decreased variability 

in salinity from land to reef also support this 

concept. There were no trends in either TP 

or CHLA with distance from land.

Another observation is that the backcountry 

exhibits elevated levels of DIN, TOC, turbidity, TP and CHLA (Figure 6.11). These distributions are driven by the southwest Florida 

shelf waters moving through this area (median DIN=0.7 μM, TOC=298 μM, Turbidity=6.4 

NTU, TP=0.48 μM, and CHLA=1.6 μg l-1). 

In addition to south west Florida Shelf influence, elevated NO3

-

 is a regular feature 

of backcountry waters, where some of the 

highest concentrations are observed in nonpopulated areas and is probably the result 

of the benthic flux of nutrients in this very 

shallow water column.

The third result is that TP concentrations 

drive phytoplankton biomass (Figure 6.12). 

Highest CHLA concentrations are seen on 

the southwest Florida shelf with a strong 

gradient towards the Marquesas and Tortugas. This is due to higher TP concentrations 

as a result of southward advection of Gulf of 

Mexico waters along the coast with entrainment of coastal rivers and runoff.

Finally, trends in water quality showed most 

variables to be relatively consistent from 

year to year, with some showing seasonal 

excursions. Overall, there were statistically 

significant decreases in DIN, TON (except 

for increases in Tortugas), TP, TOC and DO 

throughout the region (Figure 6.13). This is 

contrary to some of the trend analyses reported in previous years. 

Large changes have occurred in FKNMS 

water quality over time, and some sustained 

monotonic trends have been observed (Figure 6.13). However, trend analysis is limited 

to the window of observation; trends may 

change or even reverse, with additional data 

collection. This brings up another important 

point; when looking at what are perceived 

to be local trends, we find that they seem to 

occur across the whole region but at more 

damped amplitudes. This spatial autocorrelation in water quality is an inherent property 

of highly interconnected systems such as 

VARIABLE DEPTH MEDIAN MIN MAX n

Nitrate (μM)

Surface 0.09 0.00 5.90 6385

Bottom 0.08 0.00 5.01 3884

Nitrite (μM)

Surface 0.04 0.00 0.71 6394

Bottom 0.04 0.00 1.73 3891

Ammonium (μM)

Surface 0.29 0.00 10.32 6391

Bottom 0.25 0.00 3.88 3886

Total Nitrogen (μM)

Surface 11.76 0.73 213.21 6387

Bottom 9.84 0.88 153.75 3857

Total Organic Nitrogen 

(μM)

Surface 11.19 0.00 212.89 6363

Bottom 9.31 0.00 153.43 3830

Total Phosphorus (μM)

Surface 0.19 0.00 1.78 6396

Bottom 0.17 0.00 1.50 3871

Soluble Reactive Phosphorus (μM)

Surface 0.02 0.00 0.56 6379

Bottom 0.02 0.00 0.39 3879

Alkaline Phosphatase 

Activity (μM h-1)

Surface 0.06 0.00 5.62 6230

Bottom 0.05 0.00 0.50 3724

Chlorophyll a (μg l-1) Surface 0.23 0.00 15.24 6395

Total Organic Carbon 

(μM)

Surface 178.01 18.38 1653.5 6388

Bottom 151.13 0.00 2135.8 3867

Silicate (μM)

Surface 0.64 0.00 127.11 6089

Bottom 0.42 0.00 30.20 3692

Turbidity (NTU)

Surface 0.63 0.00 37.00 6350

Bottom 0.50 0.00 16.90 3907

Salinity (ppt)

Surface 36.2 26.7 40.9 6306

Bottom 36.2 27.7 40.9 6275

Temperature (°C)

Surface 27.1 15.1 39.6 6313

Bottom 26.7 15.1 36.8 6282

Dissolved Oxygen 

(mg l-1)

Surface 5.9 0.1 14.5 6278

Bottom 6.0 1.4 13.9 6229

Light Attenuation 

Coefficient (m-1)

0.204 0.000 4.084 4363

Dissolved Oxygen Saturation (%)

Surface 88.5 1.2 226.2 6277

Bottom 88.7 19.3 207.0 6227

Water Column 

Stratification (kg m-3)

0.01 -4.42 6.64 6256

Table 6.2. Values and sample stations (n) for water quality variables measured in 

the FKNMS, March 1995 and December 2006. Source: Boyer and Briceño, 2006.

Figure 6.10. Median nitrate concentrations (μM) in the Backcountry for the period 

1995 to 2005. Source: Boyer and Briceño, 2006.
The State of Coral Reef Ecosystems of the Florida Keys

171Florida Keys

coastal and estuarine ecosystems driven by similar hydrological and climatological forcings. It is clear that trends observed inside the FKNMS are influenced by regional conditions outside Sanctuary boundaries.

The large scale of this monitoring program has allowed a holistic view of broad physical/chemical/biological interactions 

occurring over the South Florida region. Much information has been gained by inference from this type of data collection 

program; major nutrient sources have be confirmed, relative differences in geographical determinants of water quality 

have been demonstrated and large-scale transport via circulation pathways has been elucidated. In addition, this program 

demonstrates the importance of looking “outside the box” for questions asked within. Rather than thinking of water quality monitoring as a static, non-scientific pursuit, it should be viewed as a tool for answering management questions and 

developing new scientific hypotheses. Downloadable contour maps, time series graphs and interpretive reports from the 

Southeast Environmental Research Center’s Water Quality Monitoring Network (which includes Florida Bay, Whitewater 

Bay, Biscayne Bay, Ten Thousand Islands and Southwest Florida Shelf) are available at http://serc.fiu.edu/wqmnetwork

.

Figure 6.12. Distribution of median concentrations of CHLa (left panel) and TP (right panel) in Florida’s coastal waters for the period 

1995 to 2005. Sampling stations are indicated with a plus (+) symbol. Source: Boyer and Briceño, 2006.

Elevated DIN and Turbidity in Inshore Waters

0.0

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TP CHLA Salinity

Figure 6.11. Nutrient concentration gradients from alongshore to offshore in Keys reef tract and Tortugas. Red circles denote significant 

gradient. Box plot shows data distribution and median (notch) of Keys Alongshore (KA), Hawk Channel (KC), and Reef Tract (KR) as 

well as Tortugas Alongshore (TA), Channel (TC) and Offshore (TO). Source: Boyer and Briceño, 2006.
The State of Coral Reef Ecosystems of the Florida Keys

172Florida Keys

Figure 6.13. Trends in water quality variables throughout the region from 1995 to 2005. Slopes of individual regressions at each station 

are plotted. Significant decreasing trends are shown in blue while increasing trends are in pink. Sampling stations are indicated with a 

plus (+) symbol. Source: Boyer and Briceño, 2006.
The State of Coral Reef Ecosystems of the Florida Keys

173Florida Keys

Benthic Habitats

Coral Reef Evaluation and Monitoring Project (CREMP)

The Florida Fish and Wildlife Research Institute collects annual data on the status of coral habitats in the Florida reef tract 

through the CREMP. In 1996, data collection began at 40 sites in the Florida Keys. The project was expanded in 1999 

to include three sites in the Dry Tortugas. In 2003, 10 additional sites were selected at reefs along Florida’s southeast 

coast and have been monitored annually under the Southeast Florida CREMP (SECREMP) project; the results of the 

SECREMP work are reported in the Southeast Florida chapter of this report. 

CREMP sites encompass four reef habitat categories: hardbottom, patch reef, and offshore deep and shallow reefs. Sites 

are comprised of two to four permanent stations. Data collection at each station includes an inventory of stony coral species, video transects to assess percent cover of stony coral species and selected benthic functional groups (calculated 

from images extracted from video), a qualitative assessment of disease and bleaching and a bioeroding sponge survey. 

Details on sampling design, field methods and data processing and analyses are available at http://ocean.floridamarine.

org. Previous reports have documented trends from the project initiation until 2002 (Andrews et al., 2005). This summary 

will focus on changes observed in coral communities between 2002 and 2005. 

Stony coral species richness within the 

CREMP stations showed a general decline 

across all habitat types between 1996 and 

1999 (Figure 6.14). Between 2005 and 

2006, the data show a greater decline in 

species richness at deep offshore and hardbottom sites than at shallow offshore or 

patch reef sties in the FKNMS. Some of the 

smaller or less common species have declined in distribution. For example, in 2006, 

Favia fragum, Mycetophyllia lamarckiana, 

Leptoseris cucullata and Eusmilia fastigiata were observed in approximately half of 

the stations in which they were recorded in 

2005. Overall there has been a net loss in 

species richness within the FKNMS since 

the project’s inception. Coral cover at reefs 

that were historically dominated by acroporid species (Acropora cervicornis or A. palmata) have been largely reduced to rubble 

from disease and hurricanes. The Dry Tortugas has historically supported some of 

the largest populations of A. cervicornis in 

Florida, creating large Acropora-dominated 

patch reefs (Davis, 1982). One of the most 

luxurious of these acroporid reefs was White 

Shoal patch reef where coral rubble now 

comprises a large portion of the substrate. 

A. cervicornis populations in the Dry Tortugas have decreased since the beginning of 

monitoring in 1999.

The relative mean percent cover of stony 

corals in the FKNMS declined between 

1996 and 1999, but was relatively stable 

from 1999 to 2005 (Figure 6.15). Additionally, between 2005 and 2006 there was a 

consistent loss of stony coral cover in all regions and habitats sampled in the FKNMS, 

with the deep offshore reefs showing the 

greatest decline. This observed decline 

is likely attributable to loss of cover of the 

boulder star coral, Montastraea annularis. 

This framework builder has been the dominant species in terms of percent cover and 

occurrence throughout the sites sampled in 

the Florida Keys reef system, and has been in decline throughout the duration of the monitoring project. 

Figure 6.15. Mean percent cover of stony corals by habitat within the FKNMS. Hardbottom (n=9), deep reefs (n=26), shallow reefs (n=39), patch reefs (n=29). Error 

bars represent standard error of the mean. Source: CREMP. 

0%

5%

10%

15%

20%

25%

1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006

percent Cover of Stony Corals

Hardbottom

Deep

Shallow

Patch

Figure 6.14. Mean number of stony coral species by habitat within the FKNMS. 

Hardbottom (n=9), deep reefs (n=26), shallow reefs (n=39), patch reefs (n=29). Error bars represent standard error of the mean. Source: CREMP.

0

5

10

15

20

25

1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006

number of Stony Coral Species

Hardbottom

Deep

Shallow

Patch
The State of Coral Reef Ecosystems of the Florida Keys

174Florida Keys

The hurricanes and tropical storms that affected Florida in 2004-2005 undoubtedly 

impacted coral habitats. At such a high frequency of occurrence, there has been minimal time for recovery between storms. In 

2005, hurricanes Dennis, Katrina, Rita and 

Wilma each passed over some part of the 

Florida reef tract. In some locations, structural damage to reefs can be attributed to 

storm effects; however, storm damage may 

not always be obvious. Strong waves move 

sand that can scour or temporarily suffocate 

corals, causing tissue loss without structural 

destruction. The summer of 2005 was also 

marked with periods of unusually calm conditions, which in combination with elevated 

temperatures (>31°C) caused a severe 

bleaching event in the Florida Keys. Ironically, the hurricanes also caused the water 

temperatures to drop below critical bleaching temperatures. The combination of hurricanes and severe bleaching in 2004/2005 is 

likely primarily responsible for the observed 

decrease in stony coral species richness 

and percent cover at the CREMP monitoring sites in 2006. However, the offshore deep sites, which might be expected to 

be buffered by the effects of hurricanes and bleaching, showed the greatest loss between 2004 and 2006. Since 2002, 

disease has generally decreased within the CREMP stations within the FKNMS. Diseases can be difficult to distinguish 

in the field since different pathogens can produce similar symptoms. For CREMP, the white diseases (white plague, white 

pox, white band) are placed in one category, black band in another, and the remainder in an “Other” category. The number 

of stations affected with white diseases peaked to more than 80% in 2002, subsided to 35% in 2005, then increased again 

to 50% in 2006. The number of stations affected with “Other” diseases peaked to 90% in 2001, but declined to 57% by 

2006 (Figure 6.16). These data provide information on prevalence, but not on infection rates within the stations. Also, the 

absence of the disease may indicate the death of colonies that had previously been reported as infected. Despite these 

caveats, the data indicate that stony coral diseases generally declined from 2002 levels in the Florida Keys. 

Throughout their development, coral reefs have experienced acute (and sometimes catastrophic) events such as anomalous bleaching and hurricanes. Between these events, healthy reefs begin to recover, albeit slowly. However, since monitoring began, the CREMP has not documented significant increases in coral cover at any of the study sites. This lack of 

recovery could be attributed to chronic environmental changes, from cumulative effects of hurricanes, severe bleaching 

and disease outbreaks, or a synergy of both chronic and acute impacts. Distance from human habitation has been considered a buffer from the affects of anthropogenic impacts; however, globally there are many examples of reefs that are 

remote from civilization and are similarly in decline. 

Acroporid Species in the Upper Keys

The declines in abundance of two of the principal Caribbean reef-building corals, staghorn (A. cervicornis) and elkhorn 

coral (A. palmata), are often-cited examples of the changes in western Atlantic reefs that have occurred over the past 

several decades (Aronson and Precht, 2001; Gardner et al., 2003). The causes of these declines, which began in the late 

1970s, include large-scale factors such as coral bleaching and disease, especially white band disease, as well as smaller 

scale effects related to storms and predation from corallivorous snails and damselfishes. Both corals have been under 

consideration for addition to the U.S. Endangered Species List since the early 1990s and were formally added to the list 

as threatened in 2006 based upon Caribbean-wide population declines and poor recovery.

To help support NOAA’s efforts to ascertain the current status of both Acroporid corals, scientists from the Center for Marine Science, University of North Carolina-Wilmington (UNCW) undertook an intensive assessment of the spatial distribution, colony abundance, size, and condition of staghorn and elkhorn corals in a portion of the FKNMS. During August 1-18, 

2006, a total of 107 sites were surveyed in the upper Keys region of the FKNMS from the southern boundary of Biscayne 

National Park to offshore of Tavernier, a distance of approximately 46 km along the Florida reef tract (Figure 6.17). The 

2006 surveys were an outgrowth of previous efforts conducted by UNCW dating back to 1999 to quantify the abundance 

and condition of coral reef benthos throughout the FKNMS, including the Tortugas region. Previous surveys from southwest of Key West to Biscayne National Park include 80 sites sampled in 1999, 45 sites in 2000, 108 sites in 2001, and 

195 sites in 2005; more than 100 sites were also surveyed in the Tortugas region. In 2007, the program was expanded 

throughout the Florida Keys. More information and project results can be found at http://people.uncw.edu/millers/.

Figure 6.16. Occurrence of Black Band disease, White disease and “Other” disease by station within the Florida Keys National Marine Sanctuary (n=103 stations). 

Source: CREMP.

0

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50

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70

80

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1997 1998 1999 2000 2001 2002 2003 2004 2005 2006

number of Stations

Black Band

Other disease

White disease
The State of Coral Reef Ecosystems of the Florida Keys

175Florida Keys

The objectives of the sampling design in the upper Keys region of the FKNMS were to provide information on:

•	 Habitat-based presence-absence distribution patterns encompassing diverse hard-bottom and coral reef habitat types 

from 1 to 15 m depth, including a photographic archival record of where both species were found;

•	 Colony density by site, habitat type and protection level that incorporated all of the existing FKNMS no-take marine 

reserves in the upper Keys;

•	 Size distribution of colonies in terms of tissue surface area relative to habitat type;

•	 Prevalence of colony conditions (normal/healthy, bleaching, disease, predation);

•	 Population abundance estimates for both species that is habitat and size structured; and

•	 Density and size of urchins, a continuing effort to monitor recovery of the historically abundant Diadema antillarum.

Results and Discussion

A. cervicornis was observed in the general survey area 

at 19 of the 107 sites (18%) and was recorded within belt 

transect boundaries at 16 sites. The habitat distribution 

of this coral was limited to five of the eleven habitat types 

sampled: mid-channel patch reefs (four of 14 sites, 29%), 

offshore patch reefs (10 of 23 sites, 43%), shallow (<6 m) 

low-relief hard-bottom (one of nine sites, 11%), inner line 

reef tract spur and groove (one of eight sites, 13%), and 

high-relief spur and groove (three of 17 sites, 18%). A total 

of 71 staghorn coral colonies were counted within the belt 

transect boundaries in five of the habitat types. Of these, 

five colonies (7.0%) were counted from 14 mid-channel 

patch reefs (13.1% of sampling effort), 47 colonies (66.2%) 

from 23 offshore patch reefs (21.5% of sampling effort), 10 

colonies (14.1%) from nine shallow (<6 m) low-relief hardbottom (8.4% of sampling effort), four colonies (5.6%) from 

eight inner line reef tract spur and groove sites (7.5%), and 

five colonies (7.0%) from 17 high-relief spur and groove 

sites (15.9%). These data indicate that the distribution patterns of staghorn coral were not proportional to the sampling effort and thus suggest a preferential distribution of 

this coral. A greater number of colonies than expected (if 

the habitat distribution is random) were recorded from the 

two patch reef habitat types, while fewer colonies than expected were recorded from high-relief spur and groove and 

six of the other habitat types where no colonies were recorded. The greatest mean (± 1 SD) site level densities of 

0.333 ± 0.667 colonies/m2 and 0.183 ± 0.240 colonies/m2

were recorded from two offshore patch reefs, one in the 

western area of Carysfort/S. Carysfort Sanctuary Preservation Area (site #83), the other on Mosquito Bank (site #26; 

Figure 6.18). Overall habitat-level densities were greatest 

on offshore patch reefs (0.034 ± 0.079 colonies/m2). Figure 6.17. In 2006, surveys for Acroporid corals were conducted 

at 107 sites in the northern FKNMS. Source: Miller et al., 2006b.

Figure 6.18. Mean colony density of Acropora cervicornis (left) and A. palmata abundance by size class (right) in the upper Florida 

Keys during 2006, as determined from surveys of four 15-m x 1-m transects per site at 107 sites from northern Key Largo to Tavernier, 

Florida. Error bars represent one standard error. Colonies were considered to be continuous patches of live tissue. Source: Miller et 

al., 2006b. 

0

500,000

1,000,000

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number of Colonies (± 95% CI*)

0

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>2000

Colony Size Class (cm2)

number of Colonies (± 95% CI*)
The State of Coral Reef Ecosystems of the Florida Keys

176Florida Keys

No staghorn coral thickets larger than approximately 0.5 m in diameter were observed at any location, and most sites with 

living staghorn coral colonies consisted of mostly small branches. Colony size (live tissue surface area) ranged from 7.4 

cm2 to 127.5 cm2 and was largest on mid-channel patch reefs and inner line reef tract spur and groove. Nearly 90% of 

the sampled colonies were less than 100 cm2 in surface area. Of the staghorn colonies measured, only one colony from 

the 77 assessed (1.4%) at all sites had obvious signs of damselfish predation. No incidences of white band, white pox or 

lesions were recorded for staghorn coral during the surveys.

A. palmata was observed at 18 of the 107 sites (17%) and was recorded within belt transect boundaries at 15 sites. The 

habitat distribution of this coral was limited to four of the eleven habitat types sampled: offshore patch reefs (two of 23 

sites, 9%), shallow (<6 m) low-relief hard-bottom (one of nine sites, 11%), inner line reef tract spur and groove (six of eight 

sites, 75%), and high-relief spur and groove (nine of 17 sites, 53%). A total of 388 elkhorn coral colonies were counted 

within the belt transect boundaries in four of the 11 habitat types sampled. Of these, 51 colonies (13.0%) were counted 

from among 23 offshore patch reefs (21.5% of sampling effort), 15 colonies (3.9%) from nine shallow (<6 m) low-relief 

hard-bottom (8.4% of sampling effort), 100 colonies (25.8%) from eight inner line reef tract spur and groove sites (7.5%) 

and 222 colonies (57.2%) from 17 high-relief spur and groove sites (15.9%). Clearly the distribution pattern of elkhorn 

coral with respect to habitat type was not proportional to the sampling effort, indicating a preferential habitat distribution. 

A greater number of colonies than expected (if the habitat distribution is random) were recorded from inner line reef tract 

and high-relief spur and groove habitat types. The greatest mean (± 1 SD) site level densities were recorded from highrelief spur and groove reefs at South Carysfort (site #79, 1.967 ± 2.593 colonies/m2

) and Sand Island (site #66, 1.100 

± 1.343 colonies/m2) and an inner line reef tract site at Horseshoe Reef (site #241, 0.933 ± 1.652 colonies/m2). Overall 

habitat-level densities were greatest on high-relief spur and groove and inner line reef tract habitat types.

Elkhorn coral colony sizes showed a significantly greater range compared to its congener, and several sites with large 

(>0.5 m diameter) colonies were recorded. Colony sizes (live tissue surface area) ranged from 46.3 cm2 to over 2,000 

cm2 and were greatest on high-relief spur and groove and inner line reef tract habitats. Of the 387 colonies measured, 

46% were smaller than 100 cm2 in surface area, while about 16% were greater than 500 cm2 in surface area. While most 

colonies were less than 100 cm2 in tissue surface area, larger colonies were also relatively common.

Of the elkhorn colonies measured, the most obvious impacts to live tissue were predation by snails (Coralliophila abbreviata) and damselfishes (family Pomacentridae). Lobster trap rope was found entangled in thickets of live colonies at 

South Carysfort Reef, but in general there was an absence of visible diseases such as white band and white pox. Of the 

388 colonies assessed for disease and predation, none were found with any visible symptoms of white band, white pox or 

tissue necrosis. For all sites and habitats combined, 13 colonies (3.4%) were impacted by snail predation and 11 colonies 

(2.8%) had visible lesions from damselfish predation.

Demographic Monitoring Of Acropora Palmata In The Upper Keys 

There are many monitoring studies presently in place to assess the general status and trends of Caribbean coral reefs. 

A. palmata is often poorly represented in these studies since its natural distribution is along the reef crest and many 

studies focus survey efforts on fore reef areas. Furthermore, these studies typically survey randomly placed transects 

which are not well suited to capture information on A. palmata’s presently sparse and highly patchy distribution. As a 

result, very small numbers of A. palmata colonies end up in the being counted in general reef monitoring studies. While 

this accurately depicts the present densities of Acropora, it yields very little information on the condition and fate of these 

remaining colonies. A targeted demographic (i.e., colony-based) monitoring approach (Williams et al., 2006) was used 

to track the performance of randomly selected “individual” colonies over time. In this way, the relative importance of the 

many sources of mortality for populations of A. palmata can be determined because combining the prevalence of a particular threat with the subsequent fate of affected colonies (or lethality) will show the ecological importance of the various 

threats. Thus, randomly selected colonies are tagged, measured (two diameters and height), photographed, and scored 

based on the estimated percent of live tissue and the presence and severity of a particular list of “threat” conditions on a 

regular basis. The “amount of live coral” is estimated by a Live Area Index (LAI) = [mean of 3 colony dimensions]2 x [% of 

colony with live tissue]) for each colony and summed for the colonies at each site. A total of 192 colonies in 15 plots (7 m 

radius) were tagged at five reefs in the upper keys (between Carysfort and Molasses reefs) in early 2004. Surveys were 

conducted quarterly through 2006.

Results and Discussion

Overall, A. palmata populations in the upper Florida Keys display a declining trajectory between 2004 and 2006 with 

particularly acute losses observed during summer and fall of 2005 (overall approximately 50% loss; Williams and Miller, 

2006; Figure 6.19). These losses resulted from hurricane effects and subsequent disease impacts. It should be noted that 

this observed decline is based on an already critically depressed baseline value measured in 2004 (Miller, 2002).

Slight recovery has been observed between fall 2005 and summer 2006, though 37 colonies have suffered complete mortality and 31 were physically removed by the hurricanes. Although the fragments generated from colonies that were substantially broken or completely removed could potentially yield new colonies (asexual recruits), approximately 70% of the 

369 fragments counted after the passage of Hurricane Dennis were dead or loosing tissue rapidly. Recovery of live A. palmata has resulted primarily from re-growth of remnant crusts (Figure 6.20), including the formation of new branches. Less 

than 5% of the fragments observed in the study plots have successfully reattached and survived to date, and only one 
The State of Coral Reef Ecosystems of the Florida Keys

177Florida Keys

recruit that is believed to be of sexual origin 

has been observed. Thus, total recruitment 

appears to be low and does not offset the 

observed losses in the tagged colonies. 

Demographic monitoring relies on tracking 

the performance of individual colonies to 

document the threats they face and their fate 

over time. For example, parrotfish bites may 

be extremely common among a population, 

but if effects on a colony are minor, they 

may be relatively unimportant to the viability 

of the population. Management and conservation resources can be more effectively 

applied based on an understanding of the 

relative impacts of threats on populations. 

Unfortunately, between 2004 and 2006, relatively “unmanageable” threats (hurricanes 

and disease) have accounted for substantial losses of live coral tissue including entire 

colony mortality. This emphasizes the imperative for management and conservation 

resources (i.e., funding) to support immediate research efforts to determine the proximal and ultimate causes of disease impacts 

and to identify corrective actions to mitigate 

disease losses for all Caribbean corals, but 

particularly Caribbean acroporids.

Associated Biological 

Communities

Native Americans fished for reef fishes on 

Florida reefs long before the arrival of European settlers (Oppel and Meisel, 1871). Reef 

fishing accelerated in the 1920s. Following 

growing public conflicts and sharp declines 

in catches, monitoring programs at the species level began in the early 1980s (Bohnsack et al., 1994; Bohnsack and Ault, 1996; 

Harper et al., 2000, Ault et al., 2005a).

Recreational, commercial and “headboat” 

fisheries currently occur in Florida Keys waters. From a recreational standpoint, fishers include both local residents and visitors 

(FWC, 2007). Along the reef tract, the most 

commonly targeted species are members 

of the snapper-grouper complex, including 

snappers, groupers, grunts, hogfish and 

porgies. From a commercial standpoint, 

fisheries target reef and pelagic fish species, spiny lobster, stone crabs, blue crabs, 

shrimp and ballyhoo. Headboat fisheries, in 

which customers pay “by the head” to fish 

from vessels with a typical capacity of about 

10-20 people, predominantly target reef 

species.

Trends in reef fish landings for the period 1981 to 1992 were reported for the Florida Keys by Bohnsack et al. (1994). 

Depending on the year, recreational landings comprised between 40 and 66% of total landings. Reef fishes accounted 

for 58% of total fish landings, 69% of recreational landings and 16% of commercial landings. Commercial landings were 

dominated by invertebrates (spiny lobster, shrimp and stone crabs), which comprised 63% of total landings.

20%

30%

40%

50%

60%

70%

80%

90%

100%

110%

Spring 2004

Summer 2004

Fall 2004

Winter 2005

Spring 2005

Summer 2005

Fall 2005

Winter 2006

Spring 2006

Summer 2006

Fall 2006

live area Index

Carysfort

Elbow

French

KL Dry Rocks

Molasses

dennis

Wilma

Rita

Figure 6.19. Trend in Acropora palmata LAI between 2004 and 2006 in the upper 

Florida Keys National Marine Sanctuary. Each line represents mean percent of the 

original sum of LAI for 10-12 tagged colonies per 7 m radius plot (n=1 to 5 plots per 

site). A total of 192 colonies were originally tagged. Source: Williams and Miller, 

2006.

Figure 6.20. Photograph of remnant crust approximately 20 cm long. After a series 

of hurricane impacts in summer/fall 2005, this was all that remained of a colony that 

was previously over a meter tall and wide. Photo: D. Williams.
The State of Coral Reef Ecosystems of the Florida Keys

178Florida Keys

In a 2005 report to the U.S. Congress, the National Marine Fisheries Service (NMFS) classified 11 species that are landed 

in the Florida Keys as overfished (i.e., depleted below minimum standards), and 11 as subject to overfishing (i.e., being 

fished at a rate that would lead to being overfished), with some overlap between the two categories (NMFS, 2005). Included in these totals are reef-associated species such as gag (Mycteroperca microlepis), black (M. bonaci), red (Epinephelus 

morio), snowy (E. niveatus), Warsaw (E. nigritus), Goliath (E. itajara) and Nassau (E. striatus) groupers, speckled hind 

(E. drummondhayi), and red (Lutjanus campechanus) and vermilion (Rhomboplites aurorubens) snappers. Fisheries for 

Goliath and Nassau groupers and for queen conch (Strombus gigas) were closed in 1985 and remain closed today, although the Goliath grouper stock continues to indicate signs of recovery (Porch et al., 2003 and 2006) to the extent that 

considerable debate occurs regarding re-opening of that fishery.

Ault et al. (1998) assessed the status of multiple reef fish stocks and determined that 13 of 16 groupers (Epinephinilae), 

seven of 13 snappers (Lutjanidae), one wrasse (hogfish; Labridae) and two of five grunts (Haemulidae) were overfished 

according to federal (NMFS) standards (Figure 6.21). They suggested that some stocks appeared to have been chronically overfished since the 1970s, and that the Florida Keys fishery exhibits classic “serial overfishing” in which the largest, 

most desirable species are depleted by fishing (Ault et al., 1998). Ault et al. (2001) found that the average size of adult 

black grouper in the upper Keys was about 40% of its 1940 value, and that the spawning stock for this species is now less 

than 5% of its historical unfished maximum. In subsequent analyses, Ault et al. (2005a and 2005b) determined that, of 34 

species within the snapper-grouper complex for which sufficient data were available, 25 were experiencing overfishing.

Partly in response to concerns about fishing pressure, the FKNMS established a series of Sanctuary Preservation Areas 

(SPAs) in 1997. Comparison of fish and benthic communities within versus outside of SPAs is underway. The FKNMS also 

created the Tortugas Ecological Reserve (TER) in 2001 to protect coral reef ecosystem services in that area and support 

sustainable reef fisheries. The TER protects 150 nmi2 and prohibits all anchoring, fishing and other extractive activities; it 

was the largest marine reserve in North America when first implemented. Scientists at the University of Miami and NMFS 

have studied and reported on responses of coral reef fish populations to this reserve. Based on data collected during 

more than 4,000 research dives, they compared changes in the Dry Tortugas region between 1999 and 2000 before 

the reserve was established and in 2004, three years after the reserve was established (Ault et al., 2006). As predicted 

by marine reserve theory, significant regional increases in abundance for several exploited and non-exploited species 

were detected. Significantly greater abundance of large fish were found in the TER for black grouper (Figure 6.22), red 

grouper (Figure 6.22) and mutton snapper compared to the baseline period. No significant declines were detected for 

any exploited species in the reserve, while non-exploited species showed both increases and declines. Abundance of 

exploited species in fished areas on the Tortugas Bank either declined or did not change. A comparison of black grouper 

size distributions as a function of management zone is given in Figure 6.23.

On January 19, 2007 the National Park Service (NPS) established a 119 km2 (46 mi2) Research Natural Area within the 

DTNP. This area is contiguous to the northern portion of the FKNMS Tortugas Ecological Reserve and effectively expanded the marine reserve network since it also prohibited all anchoring and extraction. Ongoing research and monitoring 

are planned to ascertain whether patterns observed in protected areas in the Tortugas are due to influences of marine 

reserves, confounding effects of recent changes in fishing regulations, hurricane disturbances, or random oceanographic 

and chance recruitment events. 

Figure 6.21. Spawning potential ratio (SPR) analysis for 34 exploited species in the snapper-grouper complex from the Florida Keys for 

period 2000-2002. Dark bars indicate overfished stocks and open bars indicate stocks that are above the 30% SPR standard. Source: 

redrawn from Ault et al., 2005a.

0

10

20

30

40

50

60

70

80

90

100

BlackConeyGagGoliathGraysbyNassauRedRed hindRock hindScampSpeckled hindYellowedgeYellowfinYellowmouthBlackBlackfinCuberaDogGrayHogfishLaneMuttonRedSchoolmasterSilkVermillionYellowtailBluestripedCottonwickFrenchMargateSailorsTomtateWhite

overfishing (30% SpR)

Exploited Coral Reef Fishes 

percent Spawning potential Ratio

groupers Snappers grunts
The State of Coral Reef Ecosystems of the Florida Keys

179Florida Keys

FWC Finfish Monitoring

Florida’s Fish and Wildlife Conservation Commission 

(FWC) conducts visual censuses between April and October to monitor finfish populations along the Atlantic margin 

of the Florida Keys in waters of the FKNMS. The principal 

goal of the visual census surveys is to evaluate the relative abundance, size structure and habitat utilization of the 

reef fish species that comprise local, commercial and recreational fisheries in the Florida Keys reef ecosystem. The 

consistent application of monitoring methods and robust 

sample sizes permit meaningful statistical analysis of the 

data collected. 

Methods

For the purposes of this study, the sampling universe in the 

FKNMS was divided into six geographical zones, designated A through F, four of which (A–D) were sampled during 

the present study (Figure 6.24). A habitat-based, randomstratified site selection procedure, based upon the Benthic 

Habitats of the Florida Keys GIS maps (NOAA, 1998), was 

used to select 39 sample sites (13 in Zone A, 10 in Zone 

B, 6 in Zone C and 10 in Zone D) each month. Sampling 

sites were randomly selected using a one longitudinal by 

one latitudinal minute grid (approximately 1 nmi2

) system. 

One mile square grids containing areas defined as “Patch 

Reefs” and “Platform Margin Reefs” were included in the 

sampling universe, with further random selection of one of 

100 “micro-grids” within each selected sampling grid (Figure 6.24). Within each grid chosen for sampling, a second 

random selection of one of one hundred 0.1′ x 0.1′ “microgrids” (approximately 0.01 nmi2

) determined the nominal 

location within the grid, providing that micro-grid contained 

reef or patch reef habitat adequate for sampling purposes 

(Figure 6.24). If this was not the case, a randomization procedure was used to relocate the sample to a nearby micro-grid with the desired habitat.

0.30

0.25

Frequency 0.20

0.15

0.10

0.05

0.00

0-9 10-19 20-29 30-39 40-49 50-59 60-69 70-79 80-89 90-99 100- 110-

109 120

0.35

0.30

0.25

0.20

0.15

0.10

0.05

0.00

0-9 10-19 20-29 30-39 40-49 50-59 60-69 70-79 80-89 90-99 100- 110-

109 120

2004

n=558

abundance=621,662

Frequency

43.4%

length (cm)

Baseline 1999-2000

n=209

abundance=277,455

14.6%

Black grouper 

Figure 6.22. Black grouper (Mycteroperca bonaci; left panels) and red grouper (Epinephelus morio; right panels) size distributions from 

the Tortugas region in 1999-2000 (top) and 2004 (bottom), before and after the establishment of the TER in 2001. Blue bars represent 

size classes larger than the minimum legal minimum size. Percentages show the proportion of the population larger than the legal 

minimum size of capture. Source: redrawn from Ault et al., 2006. 

0.35

0.30

0.25

0.20

0.15

0.10

0.05

0.00

0-9 10-19 20-29 30-39 40-49 50-59 60-69 70-79 80-89 90-99 100- 110-

109 120

0.35

0.30

0.25

0.20

0.15

0.10

0.05

0.00

0-9 10-19 20-29 30-39 40-49 50-59 60-69 70-79 80-89 90-99 100- 110-

109 120 length (cm)

Baseline 1999-2000

n=735

abundance=1,260,321

2004

n=702

abundance=1,236,584

uencyqFre Frequency

23.8%

44.6%

Red grouper 

0.35

0.30

0.25

0.20

0.15

0.10

0.05

0.00

0-9 10-19 20-29 30-39 40-49 50-59 60-69 70-79 80-89 90-99 100- 110-

109 120

ycneuqerF

0.35

0.30

0.25

0.20

0.15

0.10

0.05

0.00

0-9 10-19 20-29 30-39 40-49 50-59 60-69 70-79 80-89 90-99 100- 110-

109 120

0.35

0.30

0.25

0.20

0.15

0.10

0.05

0.00

0-9 10-19 20-29 30-39 40-49 50-59 60-69 70-79 80-89 90-99 100- 110-

109 120

length (cm)

ycneuqerF ycneuqerF

2004

Tortugas Bank, Fished 

n=16

2004

Tortugas Bank, nTmR 

n=140

2004

dry Tortugas np

n=402

18.8%

64.0%

37.3%

Figure 6.23. Black grouper size distributions in 2004 from fished 

(top) areas on the Tortugas Bank, unfished (middle) areas in the 

NTMR and recreational angling areas in the DTNP (bottom). Blue 

bars indicate size classes larger than minimum legal size; percentages show the proportion of the population larger than legal minimum size. Source: redrawn from Ault et al., 2006. 
The State of Coral Reef Ecosystems of the Florida Keys

180Florida Keys

In 1999 and 2000, data was collected using both belt transects and point counts. From 2001-2007, only stationary visual 

point counts were used. In this method, a stationary diver records the number of individuals of each target species that are 

observed within an imaginary 5 m radius cylinder and assign length intervals to each. Two divers conduct a total of four 

point counts at each site. During the visual survey, each diver lays out a 25 m tape in a pre-determined direction opposite 

from the other diver. The tapes are laid as straight as possible within the same habitat type, with at least a 15 m distance 

between each point count. The first count is conducted at the 10 m mark, and a second count is conducted at 25 m. If 

suitable habitat is not present at the designated mark then the distance is adjusted accordingly. At each survey point, the 

diver stops and remains still for two minutes, allowing for a settling period. During this time period, the diver records depth, 

substrate, habitat type, relief, complexity, percent and type of biotic coverage within the area to be surveyed, which is the 

cylindrical area extending out 5 m from the center point and from the substrate to the surface. After the settling period, the 

diver records the time and begins estimating the number of fish in each five-centimeter size class for all the target species 

present. The diver has three minutes to allow the fish to naturally redistribute themselves and to list the target species 

present within the survey cylinder. This time period also allows for cryptic species to reveal themselves for counting. The 

target species include 54 species of commercial and recreational importance that are members of the following families: 

Haemulidae (13 species); Serranidae (13 species); Lutjanidae (nine species); Chaetodontidae (seven species); Balistidae (three species); Labridae (three species); Phomacanthidae (two species) and Priacanthidae (two species). 

Results and Discussion

Overall mean densities (number of fish/100 

m2) observed from point counts ranged 

from 37 fish/100 m2 in 2000 to a high of 69 

fish/100 m2 in 2003. Overall mean densities 

have been increasing since 2001 (Figure 

6.25) and were higher in Zone C and lower 

in zone D. A total of 273,191 animals of the 

target species were recorded during 6,454 

point count surveys between 1999 and 

2006 (Table 6.3). 89% of these fish were 

from the smallest size classes (>5 to 20-25 

cm range). Fish in the family Haemulidae 

strongly dominated the point count observations, accounting for 67.6% of all individuals 

recorded, with Haemulon plumieri, H. aurolineatum, H. sciurus and H. flavolineatum, 

comprising 58.7% of the total number of 

haemulids (Table 6.3). 

Overall length-frequencies observed during point counts have been largely similar 

between years for most species. Length 

ranges and size distributions for economically important species such as Ocyurus chrysurus, Lutjanus griseus, L. maximus, Epinephelus morio and Mycteroperca 

bonaci have been very consistent through the years sampled. Only a small percentage of groupers and snappers were 

Figure 6.24. Map of Fisheries-Independent Monitoring Program sampling areas divided into four zones (A-D), in the FKNMS (left), representing a habitat-based, random-stratified site selection procedure based upon FDEP and NOAA’s (1998) mapping product “Benthic 

Habitats of the Florida Keys” (right). Source: FWC-FWRI, 2007; FDEP and NOAA, 1998.

39.2

36.9

44.2

47.6

69.0

59.9

54.5

0

10

20

30

40

50

60

70

80

1999 2000 2001 2002 2003 2004 2006

mean density (# fish/100 m2

)

Figure 6.25. Mean fish density by year (2000-2006) as recorded during visual surveys in the Florida Keys. Source: FWC-FWRI, 2007.
The State of Coral Reef Ecosystems of the Florida Keys

181Florida Keys

observed in the larger size classes during the seven years of sampling, and these percentages varied by species and 

year. For example, observations of large individuals of E. morio decreased from 22.8% in 2004 to 16.8% in 2006; sightings of large M. bonaci, increased from 15.0% in 2004 to 16.4% in 2006. No legal-size (i.e., fish that can legally be caught 

and retained) individuals of M. microlepis were observed in 2006, compared to 11.1% in 2004. Ocyurus chrysurus showed 

a slight increase in the number of legal-size fish observed with 4.8% at or above the legal limit in 2006 compared to 3.8% 

in 2004, yet this was still lower than in 2003 (7.4%). 

MACROINVERTEBRATES

FWC Spiny Lobster Monitoring

The FWC undertook a lobster monitoring program in 1997 to test the hypothesis that no-take zones would sufficiently 

protect spiny lobster so that their average abundance and size would increase in protected zones compared to similar 

fished areas. Spiny lobster monitoring in the FKNMS began at the time of reserve establishment. 

Methods

From 1997-2001, 13 reserves and similar adjacent fished areas were surveyed during the closed and open fishing seasons. Reserves were comprised of 11 SPAs (mean size 82 ha), one large SPA (515 ha) and one 3,000 ha Ecological 

Reserve (ER) at Western Sambo. From 2002 through 2005, sampling effort at three sites including the ER was only conducted during the closed fishing season. A full survey of the 13 reserve/fished area pairs was conducted during the closed 

season of 2006, the tenth year of the reserves. Surveys consisted of 60-minute timed searches for spiny lobsters. More 

information on data collection methods can be found in Cox and Hunt (2005).

Results and Discussion:

In 1997, mean lobster size was below the legal limit in both reserves and exploited areas. Since protection, mean lobster 

size in reserves has been larger than legal size, whereas in exploited areas it remained below the legal limit in most years. 

In all years, legal-sized lobsters with a carapace length ≥76 mm found in SPAs were as large as or larger than those in 

fished areas (Figure 6.26). In most years, abundance declined in both reserves and exploited areas during the open season, but the decline was less precipitous in reserves. The decline in lobster abundance inside reserves during the fishing 

season indicates that the reserves are too small to adequately protect lobsters from harvest. 

SPECIES

NUMBER

% OCCUR

DENSITY ESTIMATE (ANIMALS/100 m2)

No. % Mean SE CV Max

Haemulon plumieri 57,017 20.9 82.4 11.50 0.55 193.82 342.82

Haemulon aurolineatum 52,227 19.1 20.3 10.17 1.16 461.30 925.01

Ocyurus chrysurus 26,162 9.6 65.9 5.75 0.32 224.87 154.49

Haemulon sciurus 28,017 10.3 41.5 5.71 0.44 309.10 291.57

Haemulon flavolineatum 22,879 8.4 41.0 4.57 0.35 310.47 226.00

Haemulon spp. 16,815 6.2 10.1 3.38 0.48 576.75 318.31

Lutjanus griseus 13,241 4.8 35.5 2.95 0.29 403.80 268.23

Lachnolaimus maximus 7,400 2.7 79.3 1.62 0.07 167.30 45.41

Lutjanus apodus 5,441 2.0 19.1 1.21 0.16 547.55 143.88

Anisotremus virginicus 4,697 1.7 47.2 0.96 0.07 285.19 56.34

Pomacanthus arcuatus 3,490 1.3 67.2 0.75 0.03 146.03 13.58

Chaetodon capistratus 3,455 1.3 52.3 0.74 0.03 145.13 7.64

Haemulon melanurum 3,693 1.4 8.5 0.72 0.13 714.10 93.90

Haemulon chrysargyreum 3,502 1.3 4.9 0.70 0.14 788.99 95.49

Pomacanthus arcuatus 3,490 1.3 67.2 0.75 0.03 146.03 13.58

Chaetodon capistratus 3,455 1.3 52.3 0.74 0.03 145.13 7.64

Subtotal 197,964 72.7 -- -- -- -- --

Totals 273,191 100.0 -- 56.03 1.99 143.90 1,141.77

Table 6.3. Catch statistics for the 15 more abundant Reef Fish Species observed during Florida Keys visual sampling, 1999-2006. 

Percent (%) is the percentage of the total observations represented by that species; percent occurrence (% Occur) is the percentage 

of samples in which the species was observed; CV is the coefficient of variation. Taxa are ranked in order of decreasing mean density. 

Source: FWC-FWRI, 2007.
The State of Coral Reef Ecosystems of the Florida Keys

182Florida Keys

In Western Sambo ER, the mean size of legal lobsters and the frequency of occurrence 

of very large lobsters, especially males, increased steadily after protection was implemented in 1997. The overall abundance of 

spiny lobsters in the reserve varied without 

trend among years, but the abundance of legal-sized lobsters during the closed season 

increased significantly in the reserve relative 

to the exploited area (Cox and Hunt, 2005). 

It is apparent that some lobsters remain in 

this larger reserve for a long period of time, 

and it appears that a residential population 

of spiny lobsters is becoming established 

within the reserve. Western Sambo ER is an 

effective fishery reserve for spiny lobsters, 

presumably because of its larger size and 

protected status.

FWC Queen Conch Monitoring in the Florida Keys

Methods

The FWC monitors the recovery of the queen conch (Strombas gigas) population in the Florida Keys by conducting belttransects in locations with known conch aggregations, including marine reserves and adjacent reference areas. All conch 

within a 2 m belt-transect (laid out across an aggregation) were counted and mapped. Density and area estimates were 

used to determine population abundance. More information on data collection methods can be found in Glazer and Delgado (2003).

Results and Discussion

Since Florida’s queen conch fishery was

closed in 1986, there have been signs that

adult queen conch have begun to recover

(Glazer and Delgado, 2003; Figure 6.27). By

2003, adult conch density had increased to

about 700 conch/ha yielding approximately

37,000 adults within breeding aggregations.

However, this trend was reversed in 2004

and 2005 as density and overall abundance

declined in both years. Since most of the

breeding aggregations are in relatively shallow water (<5 m), the active hurricane seasons during these two years may have negatively impacted the aggregations. There

was a slight rebound in density and overall

abundance in 2006 to about 600 conch per

ha and 25,500 adults.

CuRREnT ConSERvaTIon managEmEnT aCTIvITIES

Mapping

In 2000, NOAA and the Fish and Wildlife Research Institute (FWRI) released habitat maps for the Florida Keys (Figure 

6.28), representing the first large-scale effort to map coral ecosystem habitats in the Florida reef tract from Biscayne Bay 

to the Dry Tortugas. Habitats were delineated based on visual interpretation of 1991-1992 aerial photographs. 

Shallow-water coral reef ecosystems of southern Florida encompass an estimated 30,800 km2

 and extend from the Dry 

Tortugas in the Florida Keys as far north as St. Lucie Inlet on the Atlantic Ocean coast and Tarpon Springs on the Gulf of 

Mexico coast (Rohmann et al., 2005). The collaborative Southern Florida Shallow-water Coral Ecosystem Mapping Implementation Plan (MIP), released in June 2005, discusses the need to produce shallow-water (about 0-40 m depth) benthic 

habitat and bathymetric maps of approximately 13,000 km2 of critical areas in southern Florida (Figure 6.29). The plan 

was developed using extensive input from over 90 representatives of state regulatory and management agencies, federal 

agencies, universities and non-governmental organizations involved in the conservation and management of Florida’s 

coral reef ecosystems. The MIP can be obtained at http://ccma.nos.noaa.gov/ecosystems/coralreef/fl_mapping.html.

Figure 6.27. Trends in the density and abundance of adult queen conch (Strombus 

gigas) in the Florida Keys, estimated from yearly monitoring of the breeding aggregations on the back reef. Source: Glazer and Delgado, 2003.

40,000 800

Conch

30,000 600

ad

adult 

ult 

20,000 400

Co

of 

nc

number 

h/ha

10,000 200

0 0

929394959697989900010203040506

191919191919191920202020202020

Abundance

Density

Figure 6.26. Size of legal (≥76 mm carapace length) lobsters in FKNMS SPAs (blue) 

and similar fished areas (red) during the closed fishing season (July). Source: Cox 

and Hunt, 2007. 

86

85

1SE)+- 

84

Cl (mm 

83

Size 

82

mean 

81

80

1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007

FKNMS SPAs

Fishery
The State of Coral Reef Ecosystems of the Florida Keys

183Florida Keys

Since 2004, NOAA’s Center for Coastal 

Monitoring and Assessment, Biogeography 

Branch (CCMA-BB) has worked with state, 

university, and other federal partners to share 

the costs of gathering imagery and field 

data, manage contracts and other activities 

related to mapping coral reef ecosystems 

of southern Florida. Since 2005, CCMA-BB 

has purchased nearly 10,000 km2 of color, 

high-resolution, commercial satellite imagery that will be used for delineating benthic 

habitats. Figure 6.30 shows satellite imagery available as a georeferenced mosaic for 

essentially 100% of the Florida Keys. While 

efforts were made to collect during optimal 

environmental conditions, the seafloor is not 

always visible in imagery as a result of widespread turbidity and some clouds. Several 

more years may be required to obtain suitable imagery of the entire area. NOAA has 

co-registered the color and panchromatic 

satellite imagery to Florida’s 2004 Digital 

Orthophoto Quadrangles and is making it 

available through the NOS Data Explorer 

(http://oceanservice.noaa.gov/dataexplorer/

whatsnew/welcome.html).

Starting in 2007, NOS began producing maps of benthic habitats in the Hawk Channel portion of the Florida Keys. As of 

June 2008, draft maps have been completed for approximately 530 km2 of Hawk Channel. A three-year grant from the 

Florida Wildlife Legacy Initiative to NOS will be used to map an additional estimated 975 km2 of Hawk Channel. In the 

fall of 2008, NOS will begin mapping a further 335 km2 of Hawk Channel. A benthic habitat map is considered draft until 

an independent accuracy assessment and peer review is completed. The NOS intends to work with NOVA Southeastern 

University’s National Coral Reef Institute to conduct the accuracy assessment.

In April 2008, Florida’s FWC plans to complete draft habitat maps of a portion of Biscayne Bay and the Dry Tortugas. 

This mapping activity, conducted in partnership with the NPS, will focus on the patch reefs found in these areas. Highresolution aerial photography, acquired in 2005, will provide the base imagery for the Biscayne Bay characterization. The 

satellite imagery discussed above will be used for the Dry Tortugas characterization.

Figure 6.29. The yellow polygon delineates the approximately 13,000 km2 priority 

shallow-water benthic habitat mapping area of southern Florida. Source: S. Rohmann, unpub. data.

80°W

80°W

82°W

82°W

25°N25°N

Benthic Habitat

Patch Reefs

Platform Margin Reefs

Continuous Seagrass

Patchy Seagrass

Hardbottom

Bare Substrate

Unknown Bottom

Land

0 20 40 km

Figure 6.28. Nearshore habitat maps were developed by CCMA-BB based on visual interpretation of aerial photography and hyperspectral imagery. The maps were released in 2000. For additional information, visit: http://biogeo.nos.noaa.gov. Map: K. Buja. 
The State of Coral Reef Ecosystems of the Florida Keys

184Florida Keys

In April 2007, the NOS deployed a 25 ft boat equipped with an interferometric acoustic sonar system to collect bathymetry 

and associated side scan sonar imagery of the Hawk Channel in the Western Sambos Ecological Reserve southeast of 

Key West. Because it is not affected by turbidity, the interferometric sensor was able to collect data of the area despite 

poor water clarity conditions. NOS hopes to use these data to classify the more turbid portions of the Western Sambos.

Assessments, Monitoring and Research 

Assessments, monitoring and research are conducted in the Florida Keys by many groups, including local, state and federal agencies, public and private universities, private research foundations, environmental organizations and independent 

researchers. Sanctuary staff facilitates and coordinates research by registering researchers through a permitting system, 

recruiting institutions for priority research activities, overseeing data management, and disseminating findings to the scientific community and the public. 

The Water Quality Protection Program, which began in 1994 and is funded by U.S. Environmental Protection Agency, the USACE and NOAA gathers data on water quality, seagrasses, and coral reef and hard-bottom communities 

(Keller and Donahue, 2006). Information about these projects is provided throughout this report and at the following Web 

sites: http://ocean.floridamarine.org/fknms_wqpp/, http://serc.fiu.edu/wqmnetwork/FKNMS-CD/index.htm, http://www.fiu.

edu/~seagrass/ and http://www.floridamarine.org/features/category_sub.asp?id=2360.

The Marine Zone Monitoring Program monitors a system of 24 marine reserves located within the FKNMS. Implemented 

in 1997, the goal of the program is to determine whether these fully protected zones effectively protect marine biodiversity and enhance human uses related to the sanctuary. Parameters measured include the abundance and size of fish 

and invertebrates, as well as economic and human dimensions of the sanctuary and compliance with regulations. This 

program monitors changes in ecosystem structure (size and number of invertebrates, fish, corals and other organisms) 

and function (coral recruitment, herbivory, predation). Human uses of zoned areas are also tracked. A summary report on 

findings of this monitoring program and other elements of the science program of the FKNMS is available online (Keller 

and Donahue, 2006; see also Cox and Hunt, 2005; and Ault et al., 2006).

MPAs and Fully Protected Areas

A significant addition to fully protected areas in the Florida Keys came with the authorization of the General Management 

Plan of the DTNP in January 2007, which includes a no-take Research Natural Area covering 158 km2 (nearly half) of the 

DTNP. A monitoring plan for the Park including its newly revised zoning plan is being developed by NPS and FWRI staff.

Gaps in Monitoring and Conservation Capacity

A significant need in the Florida Keys is a complete, updated and high-resolution benthic habitat map as described in the 

mapping section above.

Coral Spawning Partnership 2007

An inaugural coral spawning research cruise was conducted in August of 2006, with the goals of initiating conservationbased coral research, continuing to educate scientists and students, and establishing an initial baseline of knowledge 

of coral spawning at Looe Key’s Management Area, which has been federally protected since 1981. The cruise was 

operated by FKNMS and Florida’s Department of Environmental Protection (FDEP) and supported 12 scientists and four 

students from various agencies including FDEP, EPA, NMFS, FWC, Mote Marine Laboratory, the University of Florida, the 

University of Texas at Austin, the FWRI and the World Wildlife Fund. Spawning observations of major reef building species 

Figure 6.30. Satellite imagery collections of southern Florida as of November 2006. Source: S. Rohmann, unpub. data.
The State of Coral Reef Ecosystems of the Florida Keys

185Florida Keys

are listed in Table 6.4. Participating scientists also took advantage of this event to initiate studies on coral reproduction, 

settlement and aquaculture of threatened coral species in the Florida Keys. 

Overall Conclusions and Recommendations

A large amount of coral cover has been lost in the Florida Keys over the past 12 years. Monitoring programs have shown 

an overall decline in hard coral cover of 44% at quantitatively surveyed stations. Proportionally, the major framework building corals seem to have been most affected (73% loss for Acropora palmata, and 37% loss for Montastraea annularis). 

Many of the causes of local coral decline originate beyond the jurisdiction of local resource managers. For example, algal 

blooms in the Florida Keys are influenced by nutrients and water flows from the Everglades and southwest Florida coast. 

Also, warming ocean temperatures associated with global climate change are a major factor in coral bleaching. Implementing solutions that will preserve the Florida Keys coral reef system will require action on regional and global scales.

The Florida Keys is host to several environmental monitoring programs and research projects that provide information 

useful for the development of protective policies and management strategies. Resource managers must actively work 

to collect information from these multiple sources, and also incorporate observations from local residents, to get a more 

complete picture of coral reef and related habitats.

Some of the most promising research may be in the areas of coral physiology, reproduction and genetics. These studies 

will provide information that helps predict responses to environmental conditions, identify etiology of coral diseases and 

increase the success of reef restoration projects.

The coral reef is a vital component of the tourism and fisheries-based economies of the Florida Keys, where millions of 

people congregate annually to enjoy the region’s recreational experiences and seafood harvest. Continued protection of 

this important coral reef ecosystem will benefit from broad-based stewardship and greater public awareness and support.

Table 6.4. The 2006 spawning observation timeline for reef building corals at Looe Key, Florida, USA. Source: Ritchie, unpub. data.

CORAL

SPECIES

DAY 2* DAY 3 DAY 4 DAY 5 DAY 6 DAY 7 DAY 8 DAY 9

Acropora 

palmata

___ Pre-spawn Full spawn

10:25 pm11:15 pm

Intermed 

spawn 

10:35 pm11:15 pm

___ ___ ___ ___

Acropora 

cervicornis

Post-spawn ___ ___ ___ ___ ___ ___ ___

Montastrea 

annularis

___ ___ ___ ___ ___ 11:45 pm 11:25 pm11:45 pm___

Montastrea 

faveolata

___ ___ ___ ___ ___ 9:55pm12 amHeavy spawn 

11:11 pm12:15 am

11:45 pm12 am

Montastrea 

cavernosa ___ ___ ___ ___ Pre-spawn 8:00 pm10:00 pm

Post spawn ___

Diploria 

strigosa

___ ___ ___ ___ ___ 10:35 pm10:45 pm8:30 pm12:20 pmPost 

spawn

Dendrogyra 

cylindricus

___ ___ Male spawn 

9:50 pm 

___ ___ ___ ___ ___

*Days after the first full moon in August or 2006 (August 8th).
The State of Coral Reef Ecosystems of the Florida Keys

186Florida Keys

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