Panama has an estimated 1,600 sq km of coral reefs spread along almost all of its Caribbean coast. The major Caribbean reef areas are Bocas del Toro, Colon-Isla Grande and San Blas (or Kuna-Yala). Some of the best reefs in Panama are found in the Kuna-Yala (San Blas) Reserve, managed independently of the government by the indigenous Kuna since 1938. 
The Reefs at Risk analysis suggests that all of the Panamanian reefs are under threat from human activities. The most pervasive threats are overfishing and sedimentation, both affecting 100 percent of the reefs. Marine-based activities also threaten about 35 percent of reefs, particularly around the port facilities of Bocas del Toro and Colon. Coastal development is rated as a threat to 20 percent of reefs.
Unregulated exploitation of reef-related fishing resources is decimating them and, consequently, drastically reducing the income of country’s coastal population.  Most fishing along the Caribbean coastline is subsistence,  concentrated primarily on lobster (for export as well as for domestic consumption) and there are strong indicators that the lobster is overexploited.
Indiscriminate deforestation along the coastal zone and in watersheds has increased runoff into the Caribbean and effects reefs in the central and western parts of the country.  In addition, reefs of the central coast, around Colon-Isla Grande, are degraded because of major industrial activities.  The inshore reefs at Bocas del Toro receive a high sediment load, rich in pesticides and fertilizers from mainland banana plantations.  Although marine-based pollution is harming Panamanian reefs in the west around the Bocas del Toro archipelago, these reefs still hold some of the most extensive stands of elkhorn coral remaining in the Caribbean.  Tourist development is also responsible for coral degradation at Bocas del Toro, because of coral collection, over-fishing, and direct damage from divers, anchors, and boats. 
A unique threat not captured in the Reefs at Risk analysis, however, is the traditional practice of coral mining and landfilling by the indigenous Kuna people, which has significantly modified some reefs in the Kuna-Yala area over decades.  Growing tourism has further encouraged the Kuna to extract corals to sell as souvenirs.  Extraction of coral for construction has been well documented historically in Panama from the building of fortresses and settlements (for example the City of Portobelo) in the 16th Century to the building of the Panama Canal and its associated infrastructure.
Panama’s coral reefs have been affected by sea warming and diseases. Some reefs were affected during the 1982/83 El Nino which caused coral mortality, but subsequent warming events, though causing observed bleaching of corals have had little further impact.  White band and black band disease have been regularly observed, although never in epidemic proportions or causing generalized mortality. 
Panama has four protected areas on the Caribbean side, each under a different management category. Most have a rather weak legal definition and management plans are only just being developed. Since Panama has no national laws enacting reef conservation efforts, protection and management of coral reefs and resources are inadequate. 
 H.M. Guzman, “The Caribbean coral reefs of Panama,” in Latin American Coral Reefs. J. Cort