The Caribbean Fishery Management Council is charged with managing and conserving fishery resources in the U.S. territorial waters of the Caribbean around Puerto Rico and the U.S. Virgin Islands. Its area of jurisdiction extends from nine nautical miles off the state waters of Puerto Rico, and three nautical miles off the territorial waters of the Virgin Islands. However, most fishing occurs within the territorial waters of PR and USVI, and therefore federal authority over the fisheries is limited.

The Council manages more than 140 species in 3 fishery management plans (FMPs), not including the species in the Corals and Reef Invertebrates FMP. The Shallow Water Reef Fish FMP contains 141 species or separate stocks, most of whose status with regard to overfishing is unknown. However, many stocks may have been overfished historically and species such as Goliath grouper, Nassau grouper, and queen conch are severely depleted today. Others may be subject to unsustainable fishing pressure. In 2005, NMFS concluded that fishing mortality should be reduced by at least 23-30% to address likely overfishing stock complexes such as Grouper Unit 4 and Snapper Unit 1, as well as the stock complex comprised of parrotfishes.

Currently, five stocks or stock complexes in the Caribbean region are classified as being subject to overfishing: Caribbean Grouper Unit 1, Caribbean Grouper Unit 4, Caribbean Snapper Unit 1, Caribbean Parrotfishes Complex, and Queen Conch. However, the Council has limited resources to regulate the fishery and has not employed hard catch limits as a management tool to prevent overfishing up to now.