Sampling scale and lack of attention to taxa other than scleractinian corals have limited the capacity to protect coral reefs and coral communities in Pacific Panama. The distribution of coral habitats (live coral cover) and their species richness in the largest marine protected area of Panama, the Coiba National Park (270 125 ha), is described using quadrat transects and manta tows. The species richness of scleractinian corals and octocorals was lower in coral reefs than in coral communities, and a close relationship between richness and live coral cover was observed only in coral communities. The distribution of high live coral cover in coral communities overlapped with areas of high coral species richness. Average live coral cover in communities was 64%, compared to 28% in reefs, whereas algae cover was 30% and 49%, respectively. Twenty-two coral and 34 octocoral species were observed, many only now detected in Panama as endemic or new species. Analysis of satellite imagery showed 80% of terrestrial habitats were mostly primary forest, and coral reefs and coral communities covered 1700 ha, about 2% of marine habitats. Shallow marine environments (< 20 m) had up to 60% calcareous red algae cover (rhodolite beds). Based on the distribution of live coral cover and species richness, three conservation units were identified as priority, with the southern and northernmost sides of the marine protected area as the most significant. These three areas encompass most of the rare and endemic species or populations, as well as species previously regarded as endangered.