The accelerated deterioration of coral reefs in Puerto Rico is unprecedented. During the past two years coral reefs in Puerto Rico have suffered an ecological catastrophe due to a 30 to 60% mortality of the live surface of corals that make up reefs. This was a consequence of stress associated with bleaching (the loss of symbiotic algae known as zooxanthellae) due to an unusual and prolonged warming of the water in 2005. This event was followed by a massive breakout of lethal diseases in corals. A combination of cumulative anthropogenic factors, among them the deterioration in the water quality as a consequence of historic misuse of land, the deterioration of hydrographic basins and overfishing, as well as the global warming effects, have contributed to their loss. What to do? We need start working right now in a collaborative, multidisciplinary, multisectorial and multiagency perspective. The 1979 Puerto Rico Coral Reef Inventory should be updated; we should develop a National Plan for Coral Reef Management; and complete the development of individual management plans for all protected marine areas consonant with the National Plan. Also, ecological multidisciplinary coral reef monitoring programs that respond to experimental questions and hypothesis that measure the effectiveness of management programs should be implemented; revise, update and refocus identified priorities in the Local Action Strategy Plan and include priorities such as climate change, recuperation of coral reefs and coral reef fishing. Other options include developing an initiative to recuperate coral reefs that identify priority areas for ecological restoration; identify and document the actual condition and spatial distribution of those priority coral species to develop strategies of propagation and reintroduction to the reefs; and encourage aquaculture and cultured coral transplant as strategies for propagation.