HABITAT CONSERVATION PLANNING 

AND

INCIDENTAL TAKE PERMIT PROCESSING

HANDBOOK

November 4, 1996

U.S. Department of the Interior

Fish and Wildlife Service

U.S. Department of Commerce

National Oceanic and Atmospheric Administration

National Marine Fisheries Service
TABLE OF CONTENTS

Section Page

Preface ................................................................... I

Chapter 1 - The ESA and Incidental Take Permits ................................. 1-1

A. Purpose of the Habitat Conservation Planning Process ..................... 1-1

B. Purpose of the Handbook ........................................... 1-1

C. Background and Legal Authority ..................................... 1-1

D. Coordination Between FWS and NMFS ................................ 1-3

E. Overview of the Incidental Take Permit Process .......................... 1-4

1. When is a Permit Needed? ...................................... 1-4

2. What Kinds of Activities Can Be Authorized? ....................... 1-5

3. Phases of the Process .......................................... 1-5

4. Compliance With NEPA and Section 7 of the ESA .................... 1-6

5. Guiding Principles ............................................ 1-7

F. Overview of Permit Processing Requirements ............................ 1-7

1. Expeditious Processing of Permit Applications ....................... 1-8

2. The Low-effect HCP Category ................................... 1-8

3. Processing Low-Effect Permit Applications ......................... 1-9

4. Summary of Permit Processing Requirements ........................ 1-9

5. Target Permit Processing Times ................................. 1-10

6. Benefits of Regional Conservation Planning ........................ 1-14

G. Helpful Hints ................................................... 1-15

Chapter 2 - Overview of FWS and NMFS Roles and Responsibilities ................... 2-1

A. Delegation of Permit Authority ....................................... 2-1

B. Roles and Responsibilities ........................................... 2-1

1. Applicant ................................................... 2-1

2. Field Office ................................................. 2-2

3. Regional Office .............................................. 2-3

4. Washington Office ............................................ 2-7

5. Solicitor’s Office/General Counsel Office ........................... 2-7

Chapter 3 - Pre-application Coordination and HCP Development ...................... 3-1

A. Getting Started .................................................... 3-1

1. Who Can Apply for a Section 10 Permit? ........................... 3-1

2. Determining the Appropriate Applicant ............................ 3-2

3. Steering Committees .......................................... 3-3

4. The Services' Role on Steering Committees & HCP Efforts ............. 3-4

5. Preparing the HCP Species List .................................. 3-7

6. Involving Other Federal and State Agencies ......................... 3-8

7. Treaty Rights and Trust Responsibilities ............................. 3-

B. Developing the HCP ............................................... 3-

1. Mandatory Elements of an HCP ................................... 3-
TABLE OF CONTENTS (CONT.)

Section Page

2. Identifying Project Impacts ....................................... 3-

a. Delineation of HCP Boundaries ............................... 3-

b. Collection and Synthesis of Biological Data ...................... 3-

c. Determination of Proposed Activities ........................... 3-

d. Determining Anticipated Take Levels ........................... 3-

e. Coordinating the HCP With Section 7 of the ESA ................. 3-

f. Addressing Indirect Project Effects ............................ 3-

g. Consideration of Plants in the HCP and Permit .................... 3-

h. Addressing Effects on Critical Habitat .......................... 3-

3. Mitigation Programs & Standards ................................. 3-

a. Regulatory Standards & Relationship to Recovery ................. 3-

b. Must an HCP Benefit the Species? ............................. 3-

c. Mitigation For Habitat Loss .................................. 3-

d. Funding Recovery Measures as Mitigation ....................... 3-

e. Mitigation for Small-Scale, Low-Effect Projects .................. 3-

f. Consistency in Mitigation Standards ........................... 3-

g. Adaptive Management ...................................... 3-

4. Monitoring Measures ........................................... 3-

5. Unforeseen/Extraordinary Circumstances ............................ 3-

a. The "No Surprises" Policy ................................... 3-

b. HCP Amendments ......................................... 3-

6. Funding ..................................................... 3-

7. Analyzing Alternatives .......................................... 3-

8. Additional Measures-Implementing Agreements ....................... 3-

C. Alternative HCPs .................................................. 3-

1. Addressing Species Through Habitat-Based HCPs ..................... 3-

2. Programmatic HCPs ............................................ 3-

D. Addressing Migratory Birds and Eagles (FWS Only) ........................ 3-

E. Coordinating HCPs With National Wildlife Refuges (FWS Only) .............. 3-

F. "Safe Harbor" Policy ............................................... 3-

Chapter 4 - Treatment of Unlisted Species ....................................... 4-1

A. Addressing Unlisted Species in the HCP ................................ 4-1

1. Deciding How to Address Unlisted Species ......................... 4-2

2. Addressing Unlisted Species in the HCP and Permit ................... 4-2

3. Standards for "Covering" Species Under a Permit ..................... 4-4

B. Challenges in Treating Unlisted Species ................................ 4-4

Chapter 5 - Environmental Analysis and Documentation ............................ 5-1

A. General Information ............................................... 5-1
TABLE OF CONTENTS (CONT.)

Section Page

1. Scope of the NEPA analysis ..................................... 5-1

2. Categorical Exclusions ......................................... 5-2

3. Environmental Assessments ..................................... 5-3

a. Use of EAs When Mitigation Reduces Significant Impacts .......... 5-3

b. Programmatic EAs ........................................ 5-4

4. Environmental Impact Statements ................................ 5-4

B. Techniques for Streamlining Section 10 and NEPA Planning ................. 5-5

1. Combining NEPA/HCP Documents ............................... 5-5

2. Joint-Federal State Process ...................................... 5-5

3. Incorporation by Reference ..................................... 5-6

C. Internal Service Guidance and Assistance ............................... 5-6

Chapter 6 - Application Requirements and Processing Procedures ..................... 6-1

A. Guidance to the Applicant ........................................... 6-1

1. What to Provide the Applicant ................................... 6-1

2. Application Form and Instructions ................................ 6-2

3. Name of Applicant ............................................ 6-2

4. Application Fee .............................................. 6-2

5. Providing the General Permit Requirements ......................... 6-3

B. Processing the Application .......................................... 6-3

1. Processing Times ............................................. 6-3

2. Timing of Document Preparation and Submission ..................... 6-4

a. Description of Required HCP Documents ...................... 6-4

b. Submitting the Complete Application Package ................... 6-5

c. Certification of Application by the Field Office ................... 6-6

d. Timing of Other Application Documents ....................... 6-6

e. Labeling the Documents as Draft/Final ......................... 6-7

f. Dating Section 10 Documents ............................... 6-8

g. Finalizing the Implementing Agreement ........................ 6-8

3. Who Submits the Application Package? ............................ 6-9

4. Judging the Application for Completeness .......................... 6-9

5. Problems Identified During HCP Development ....................... 6-9

6. FWS Law Enforcement LEMIS System ........................... 6-10

C. Internal FWS/NMFS Review ....................................... 6-10

1. Early Coordination Between Field and Regional Office ................ 6-10

2. Distribution of the Application Package ........................... 6-12
TABLE OF CONTENTS (CONT.)

Section Page

3. Internal Section 7 Consultation .................................. 6-13

a. Role of the Section 7 Consultation ........................... 6-13

b. Who Conducts the Section 7 Consultation? .................... 6-14

c. Conferences on Proposed Species ........................... 6-15

d. Biological Opinion Formats/Requirements ..................... 6-16

4. Legal Review of the Application Package .......................... 6-19

5. Preparing the Signature Package ................................ 6-19

6. New Policies or Legal Questions ................................ 6-20

D. Federal Register Notices of Receipt .................................. 6-20

1. Timing of the Notice ......................................... 6-20

2. Content of the Notice ......................................... 6-21

3. Submission of the Notice ...................................... 6-21

4. Providing HCP Documents to the Public/FOIA Considerations ......... 6-22

5. Objection to the Permit ....................................... 6-24

6. Notice of Permit Issuance, Denial, or Abandonment .................. 6-24

E. Permit Issuance Conditions & Reporting Requirements .................... 6-25

1. Permit Conditions ........................................... 6-25

2. Permit Duration ............................................. 6-25

3. Distribution of Copies of the Permit .............................. 6-26

4. Reporting Requirements ....................................... 6-26

F. Permit Denial, Review, and Appeal Procedures ............................ 6-

1. Permit Denial ............................................... 6-27

2. Review Procedures ........................................... 6-27

3. Requests for Reconsideration ................................... 6-27

4. Appeal .................................................... 6-28

5. Copies of Denials ............................................ 6-28

G. Permit Amendments .............................................. 6-29

H. Permit Renewal ................................................. 6-29

I. Permit Transferals ................................................ 6-30

J. Permit Violations, Suspensions, and Revocations ........................ 6-31

1. Notifying Law Enforcement .................................... 6-31

2. Permit Suspension/Revocation .................................. 6-32

Chapter 7 - Issuance Criteria for Incidental Take Permits ............................ 7-1

A. General Permit Issuance Criteria ...................................... 7-1

B. Endangered/Threatened Species Permit Issuance Criteria ................... 7-2

1. Taking Will Be Incidental ....................................... 7-2

a. Authorizing Take Associated With Mitigation Activities ........... 7-2

b. Authorizing Take for Scientific Purposes ....................... 7-3

2. Applicant Will Minimize and Mitigate Impacts ....................... 7-3

3. Will Ensure Adequate Funding/Unforeseen Circumstances .............. 7-4
TABLE OF CONTENTS (CONT.)

Section Page

4. Will Not Reduce Likelihood of Survival & Recovery .................. 7-4

5. Other Measures Required Will Be Provided ......................... 7-5

6. Assurances That the HCP Will Be Implemented ...................... 7-5

Chapter 8 - Definitions ..................................................... 8-1
LIST OF APPENDICES

Appendix 1: Section 10 Regulations: 50 FR 39681, September 30, 1985 (FWS); 55 FR 20603,

May 18, 1990 (NMFS). 

Appendix 2: Reference List of Publications on HCPs and Conservation Biology

Appendix 3: Example of an HCP Memorandum of Understanding 

Appendix 4: "Template" Implementing Agreement

Appendix 5: FWS Guidance on Addressing Migratory Birds and Eagles (FWS Only)

Appendix 6: FWS Guidance on Integrating HCPs With National Wildlife Refuges (FWS Only)

Appendix 7: Safe Harbor Policy

Appendix 8: Example of an Integrated HCP/EA

Appendix 9: FWS Fish and Wildlife Permit Application Form 3-200 With Privacy Act Notice,

Instructions, and Notice of Permit Application Fee; and NMFS Incidental Take

Application Instructions 

Appendix 10: General Permit Conditions: 50 CFR Part 13 (FWS); 50 CFR Parts 217, 220, and

222 (NMFS)

Appendix 11: Endangered and Threatened Species Permit Conditions: 50 CFR Part 17 excerpts

(FWS); 50 CFR 222.22 (NMFS)

Appendix 12: List of FWS/NMFS Washington, D.C. and Regional Offices

Appendix 13: Examples of a Set of Findings

Appendix 14: FWS Director's Order No. 11 and Examples of an Environmental Action

Memorandum

Appendix 15: Federal Fish and Wildlife Permit (Form 3-201)

Appendix 16: Examples of Federal Register Notice of Receipt of Permit Application and Notice

of Availability of NEPA Document

Appendix 17: Examples of Issued Incidental Take Permits

Appendix 18: "Template" Federal Register Notices of Permit Issuance
FOREWORD

It gives us great pleasure to introduce this new Habitat Conservation Planning Handbook. It is the

culmination of much hard work by dedicated U.S. Fish and Wildlife Service and National Marine Fisheries

Service employees. It represents a great deal of collaboration with our conservation partners, and an

important milestone in our ongoing efforts to make the Endangered Species Act (Act) more efficient and

effective while providing voluntary opportunities for private landowners to be involved in conservation.

With the streamlining measures and other innovations provided in this handbook, the Habitat Conservation

Planning (HCP) process ranks as one of our greatest successes in seeking ways to reduce the Act’s

regulatory burden on private landowners while addressing the habitat needs of listed species.

HCPs reduce conflicts between listed species and economic use or development activities, allowing for the

development of "creative partnerships" between the public and private sector which make the process work

for both landowners and species. We have taken a process that was rarely used and have turned it into an

increasingly utilized and successful way to provide private owners of natural resources with the creative

flexibility and certainty they need to plan their activities while providing protection for listed species.

Species benefit too, and that is another strength of this process. It often expands the focus from conserving

a single species to looking at the ecosystem as a whole, and that can often keep species from declining long

before they may need to be considered for listing. Thus, the HCP process provides many opportunities for

willing owners of natural resources to make positive contributions to the conservation of species and their

habitats. This allows landowners to become true partners in the conservation of our precious natural

heritage.

We would like to take this opportunity to express our heartfelt thanks for the hard work and dedication of

all those who have made the development of the HCP process and this handbook possible. I especially

want to thank those States, county and private natural resource owners who have become conservation

partners with our Departments through this process. This document will be an important tool in threatened

and endangered species conservation for our Nation.

Bruce Babbitt D. James Baker

Secretary Under Secretary for Oceans and Atmosphere

Department of the Interior National Oceanic and Atmospheric Administration
PREFACE

The habitat conservation planning (HCP) program under section 10(a)(1)(B) of the Endangered

Species Act (ESA) has grown rapidly in recent years. In the first 10 years of the program (1983-

1992), 14 incidental take permits were issued. As of the end of August, 1996, 179 incidental take

permits had been issued and approximately 200 HCPs were being developed. In just a few years

the HCP process has been transformed from a relatively little used option under the ESA to one

of its most important and innovative conservation programs.

Another pattern has begun to emerge, as evidenced by the growing number of HCPs being

developed and by the size of the conservation planning areas involved. As of late 1995, most

HCPs approved were for planning areas less than 1,000 acres in size. However, of the HCPs

being developed as of early 1996, approximately 25 exceed 10,000 acres in size, 25 exceed

100,000 acres, and 18 exceed 500,000 acres. This suggests that HCPs are evolving from a

process adopted primarily to address single developments to a broad-based, landscape level

planning tool utilized to achieve long-term biological and regulatory goals. It also suggests that

the underlying spirit of the HCP process has begun to take hold.

These large-scale, regional HCPs can significantly reduce the burden of the ESA on small

landowners by providing efficient mechanisms for compliance, distributing the economic and

logistic impacts of endangered species conservation among the community, and bringing a broad

range of landowner activities under the HCPs’ legal protection. In addition, the Services have

helped reduce the burden on small landowners and have made it easier for them to be involved in

the HCP process through streamlining measures in the HCP process. 

The HCP process was patterned after the San Bruno Mountain HCP--an innovative 

land-use planning effort in California's San Francisco Bay area that began in the mid-1970s with a

classic conflict between development activities and endangered species protection and culminated

in the issuance of the first incidental take permit in 1983. What made the San Bruno Mountain

case unusual was that it attempted to resolve these conflicts through negotiation and compromise

rather than continued litigation. This fundamental approach was endorsed and codified by

Congress when it incorporated the HCP process into the ESA in 1982.

One of the great strengths of the HCP process is its flexibility. Conservation plans 

vary enormously in size and scope and in the activities they address--from half-acre lots to

millions of acres, from forestry and agricultural activities to beach development, and from a single

species to dozens of species. Another key is creativity. The ESA and its implementing

regulations establish basic biological standards for HCPs but otherwise allow the creative

potential of HCP participants to flourish. As a result, the HCP program has begun to produce

some remarkably innovative natural resource use and conservation programs.

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The challenge of balancing biology with economics is a complex one, but is fundamental to the

HCP process. Policy and procedure have at times frustrated HCP users and hampered the 

program's ability to meet its full potential. The HCP process was historically viewed as

procedurally difficult; permit approvals took too long in some cases and long-term regulatory

certainty under HCPs was widely desired by applicants but rarely available.

However, the U.S. Fish and Wildlife Service and National Marine Fisheries Service have made

significant improvements in the HCP program in recent years. We have increased section 10 staff

and improved guidance about section 10 objectives and standards, clarified and streamlined permit

processing requirements, and substantially raised the certainty provided to HCP permittees. This

handbook incorporates all these improvements and reflects updated policies and procedures in the

HCP program.

The handbook is organized as follows. Chapter 1 provides a summary and overview of the HCP

process. Chapter 2 summarizes the roles of the applicant and the Fish and Wildlife Service and

National Marine Fisheries Services' Field, Regional, and Washington Offices. Chapter 3 explains

the process of developing an HCP. Chapter 4 explains how unlisted species may be addressed in

an HCP. Chapter 5 deals with section 10 NEPA requirements. Chapter 6 explains how to

process and review an incidental take permit application. Chapter 7 explains the section 10 permit

issuance criteria. Finally, Chapter 8 contains a glossary of important terms used throughout the

handbook.

The handbook also contains numerous appendices, which include pertinent Federal regulations

and policies; a reference list of publications about HCPs; "template" HCP documents that can be

used as guides; and examples of HCP documents such as a permit application form and Federal

Register notices. The handbook is organized to make information readily available. All important

issues have labeled sections or subsections. The reader can find specific subjects of interest by

scanning the Table of Contents and turning to the appropriate page.

 Acting Director

 U.S. Fish and Wildlife Service

 Assistant Administrator for Fisheries

 National Marine Fisheries Service 

ii