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The Gulf of Mexico has a dynamic ichthyofaunal community of more than 1443 finfish species, over 51 shark species, and at least 49 species of rays and skates. The Gulf of Mexico ecosystem has a relatively high biodiversity and a large number of fish and shark species compared to the Pacific and Atlantic coastal areas of the United States. Many fish stocks of great commercial and recreational importance in the Gulf of Mexico have been determined to be overfished (population levels too low) and/or in the status of overfishing. A wide variety of long-term anthropogenic and natural stressors, such as rapid coastal development, overfishing, shrimp fishery bycatch, climate change, hypoxia, and natural disasters, have negatively affected the Gulf of Mexico finfish and sharks. Of the 13 species that were selected as representative for evaluation, five species were being overfished and/or were in the status of overfishing before 2010. These five species include red snapper, red grouper (some local subpopulations), Atlantic bluefin tuna (most likely but the uncertainty is high), Atlantic blue marlin, and greater amberjack. In addition, many shark species were overfished or were in the status of overfishing immediately before or around April 2010. Management regulations adopted for many fisheries in the 2000s to limit fishing efforts, and shrimp fishery bycatch appear to have been successful for some finfish and shark species, which has reduced the number of overfished fish populations and the frequency of overfishing in the Gulf of Mexico.

The Gulf of Mexico offers ample opportunities to both commercial and recreational fishermen. Long-term landings of most key commercial species appear to be stable. Changes in landings are often tied to regulations to manage fish stocks. For the analysis of Gulf fisheries, a 20-year period from 1990 to 2009 was chosen as inclusive of (1) pre- and post-management agency changes, (2) active tropical storm periods, (3) challenging production cost situations, and (4) high and low points in the national economy. This approach acknowledges that a species’ stock level and economic conditions of inputs and demand play roles in landings levels. A 3-year average was used to depict landings and associated value. Increasing imports has led to progressive decline in brown and white shrimp fisheries where employment has dropped from 109,000 in 2007 to 63,000 in 2009 and revenues have dropped from $2.5 billion to $1.7 billion. The Gulf shrimp-processing sector has experienced a steadily eroding marketing margin that has culminated in consolidation of this sector.

Five species of sea turtles occur in the Gulf of Mexico: Kemp’s ridley (), loggerhead (), green (), leatherback (), and hawksbill (). Nesting, distribution, abundance, habitat, and life history information has been reviewed for each sea turtle species in the Gulf prior to the Deepwater Horizon oil spill in April 2010. Kemp’s ridley has made a remarkable recovery from the brink of extinction in the early 1980s. Annual loggerhead nesting on Peninsular Florida beaches in both the Gulf of Mexico and Atlantic Ocean increased from 1979 through 2000 but declined from 2001 through 2009; however, loggerhead nesting on Florida Gulf and Atlantic coast beaches in 2010 and 2011 was similar to 2000 levels, indicating that the nesting population may undergo periods of variability that may affect long-term trend predictions. Annual loggerhead nesting on Peninsular Florida beaches in both the Gulf of Mexico and Atlantic Ocean increased from 1979 through 2000 but declined from 2001 through 2009; however, loggerhead nesting on Florida Gulf and Atlantic coast beaches in 2010 and 2011 was similar to 2000 levels, indicating that the nesting population may undergo periods of variability that may affect long-term trend predictions. Leatherback sea turtles use the Gulf of Mexico as a foraging area and are often found in areas containing an abundance of jellyfish. Large numbers of leatherbacks are captured each year in the Gulf as bycatch in pelagic longline fisheries. Threats to hawksbills in the Gulf of Mexico include the destruction of nesting habitat, their dependence on coral reefs—one of the world’s most endangered ecosystems—for food and shelter, and the continued illegal trade in hawksbill products.

Fifteen indicator species with different lifestyles and behavioral patterns are used to examine the health of the Gulf avifauna before the Deepwater Horizon accident. There are 395 bird species recorded for the Gulf, and 31 % occur along all coasts of the Gulf. The highest avian diversity is along the Mexican Gulf Coast. A high proportion of the US nesting population of Reddish Egret, Sandwich Tern, Black Skimmer, Royal Tern, Forster’s Tern, Laughing Gull, Snowy Plover, and Roseate Spoonbill occur along the Gulf. Several seabirds (boobies, frigatebirds) nest primarily on the Campeche Banks in the southern Gulf of Mexico. Habitat loss, due to both anthropogenic and natural causes (sea level rise, erosion), is the primary threat facing birds in the Gulf of Mexico, followed by predators, human disturbance, high tides, storm tides, and other weather-related events. Loss of habitat is most severe at the land margin, where the land meets the sea. Pollutants have affected behavior and populations of birds in the Gulf although to a far lesser degree than habitat loss and modification. Oil can cause immediate mortality and chronic injury, but it has not been demonstrated to permanently affect any populations of birds in the Gulf. Plastics and fishing lines cause mortality, particularly in seabirds foraging in the Gulf.

Recorded knowledge of marine mammals of the Gulf began with commercial whaling of sperm whales, short-finned pilot whales, and Risso’s dolphins in the 1700s and 1800s, progressed to natural history observations and one of the first volunteer stranding organizations, the Texas Marine Mammal Stranding Network, in the 1970s. The vegetarian sirenian, the West Indian manatee (), occurs mainly in Florida. All others are cetaceans, members of the whale and dolphin clades. There are no porpoises, sea lions, fur seals, or true seals in the Gulf. The most common cetacean in the Gulf numerically is the pantropical spotted dolphin (), and the one with most biomass is the sperm whale (), common in mid-depth waters off Louisiana and the shelf break off Texas. Major anthropogenic threats exist for all marine mammals but do not appear to be as intensive in the Gulf as in several other oceanic basins. Threats to marine mammals in the Gulf include prey depletion, incidental mortality, injury due to fisheries, intentional and direct takes, vessel strikes, disturbance, acoustic (noise) pollution, chemical contamination, ingestion of solid debris, oil spills, and aspects of ecosystem change.

Most mortality results from natural causes including red tide which is primarily restricted to West Florida and cold-kills that have greater influence in the warmer regions of South Texas and South Florida, but also kill a significant amount of fish and other animals in the northern Gulf. With the exception of red tide and other harmful algal blooms, the health of the Gulf has not been systematically studied. Mexico has only recently started to evaluate the health of its coastlines. Mortalities of marine animals, particularly fishes, in the Gulf caused by natural and anthropogenic events seem to interact with infectious disease agents and noninfectious diseases, but the mortalities are often attributed to the disease agents alone. “Events” that cause mortalities include eutrophication; hypoxia; algal blooms; temperature, salinity, and weather extremes; and chemical and sediment pollution. “Diseases” include those caused by infectious agents, parasites, neoplasms, and developmental abnormalities. Interactions of the effects of diseases and stressful events are considered important but little investigated.