Probably the major concern with this fishery is the issue of bycatch, both of finfish and of turtles. Several mollusc species support valuable fisheries in the area, in particular the fisheries in the USA for cupped oysters and calico scallops. The queen conch fishery is cause for some concern, and the stock is considered to be over-exploited in most countries in the area. Mexico has the largest landings of this species. Serious attempts are being made to assess the status of the species and determine appropriate management responses.
Environmental degradation presents cause for concern in some areas and fisheries within the region.
The coastal habitats are vulnerable to on-going coastal development and to impacts from inland developments such as pollution and damming of rivers. Loss of important coastal nursery areas such as mangrove and sea grass habitats, are specific examples of problems being experienced. Coral reefs, important habitats in the region of substantial socio-economic importance through both tourism and fisheries, are also being degraded. The Final Report of the International Coral Reef Initiative Workshop in 1995 reported on incidences of declines in reef fish populations and coral cover across the region. These changes were being brought about by factors such as terrestrial runoff of both sediments and nutrients, direct physical damage to the reefs in a number of ways, and overexploitation of fish resources.