The protected sites defined under the Marine Conservation Corridor of the Tropical Eastern Pacific (MCCTEP) include most of the endemism and a fraction of the areas of high diversity for reef corals and fishes. Although those areas are connected biologically over distances >600 km, lack of large-scale sampling and attention to taxa other than scleractinian corals has limited the protection of shallow coral reef and coral community habitats in some areas of the Tropical Eastern Pacific (TEP) region, particularly non-offshore islands in Ecuador, Panama and Costa Rica. The newly created Las Perlas marine protected area (1688 km2), the second largest archipelago in the TEP, fills a regional conservation gap for the protection of reefs and potentially becomes the second highest coral diversity area in the MCCTEP. This study describes the distribution of live coral cover and species alpha-diversity over 307 ha of shallow coral reefs and coral communities in the Las Perlas Archipelago. Nineteen scleractinian and 38 octocorals were observed, including species previously thought to be uncommon. Although coral communities generally had a greater number of species than coral reefs, species richness did not differ between habitats. However, their coral and octocoral composition and benthic makeup (coral cover, macroalgae, sponge, etc.) differed. The reefs had higher live coral cover (61.2%) and lower algal cover (32.5%) than the coral communities (26.0% and 65.7%, respectively). Octocorals were more common in the communities than on the reefs. There was a negative relationship between live coral cover and species richness, low to moderate cover generally coinciding with coral community sites and higher species richness. Areas are recommended for marine reserve zoning within the new Las Perlas marine protected area to ensure the protection of important habitats and maintenance of diversity in the TEP, both highlighting the importance of the southern islands of the archipelago for coral diversity and the northern islands for their high live coral cover. Review of the representativeness of regional coral diversity would facilitate better design of small-scale reserves across the TEP, following comparable survey methods.