Cuba is the largest of the Caribbean islands (111,950 sq km), with a long, complex coastline and considerable chains of offshore islands and coral cays. Fore reefs can be found along almost the entire border of the Cuban shelf,  which extends for approximately 3200 km. In many places these fore reefs bear crest reefs at their shallowest zone. These reef crests are more abundant at the edges of the four broad sections of the Cuban shelf: Gulf of Guanahacabibes (northwest Cuba), Sabana-Camaguey Archipelago (central north Cuba), Gulf of Ana Maria-Guanayabo (southeast Cuba), and Gulf of Batanabo (southwest Cuba). Inshore, patch reefs are also found in the northwestern, southwestern and southeastern sections of the shelf. 
Overall, the Reefs at Risk analysis rates more than 70 percent of Cuba’s reefs as threatened, with over 35 percent at high threat. The threat from overfishing is estimated to be the main threat to Cuba’s reefs (over 65 percent threatened), and the landing statistics for the commercially important snapper and grouper underline this threat with decreasing annual catches and maximum size over the last 20 years because of the use of unsustainable fishing practices.  From 1970 to 1975, increased fishing effectiveness (e.g., use of trawls, seines, and set nets) resulted in overfishing of several important species (e.g., lane snapper, nassau grouper). Overfishing also resulted from the use of non-selective fishing gear, the indiscriminate use of set nets during spawning aggregations, and limited enforcement.  This situation led to the introduction of a series of drastic fishery-management regulations  and ultimately to a change in fishery administration policy.  However, the Cuban coral reef fishery today is probably in better condition than the fisheries of other Caribbean countries (higher species richness, biomass, and average size), with about 40 percent of the total commercial catch coming from the reefs.  Furthermore, in 2004, an official resolution of the Fisheries Ministry banned the use of trawl nets and set nets in Cuban waters.
About one-quarter of reefs were rated as threatened by sedimentation and pollution from inland sources, about one-fifth by coastal development, and fewer than 10 percent by marine-based sources. The low sedimentation and coastal development threats are mainly due to the offshore location of many reefs, outside the influence of land-based sources of pollution,  and to Cuba’s relatively undeveloped tourist industry. Watersheds have historically been extensively deforested, increasing the sediment runoff to the sea,  and satellite images have revealed large amounts of sediment along the southern coast of the island of Cuba, probably as a result of forest removal and agricultural practices, possibly combined with severe rains. Remote reefs (e.g., around the southern archipelagos) are in very good condition, but near large population centers such as Havana, signs of decline are evident, with low coral cover, overgrowth by algae, and disease outbreaks. 
Tourism, a prevalent impact on many reefs in the Caribbean, is relatively undeveloped in Cuba and thus has only a limited impact on Cuban coral reefs. However, the tourist diving industry is rapidly growing, there is increasing awareness of the need to deploy more mooring buoys, and the number of diving sites with such buoys is increasing (though theft of mooring buoys near population centers is a problem).  Anchoring on coral outcrops has been and continues to be a practice in fishery and other nautical activities.  The extraction of stony corals and other organisms is degrading the reefs of tourist areas where there is easy access for the general public, such as the reefs of Puerto Escondido to the northeast of Havana Province. 
Hurricanes are more frequent in the south and west, where the reef communities are dominated by species resistant to sedimentation, especially in the Gulf of Bataban