Cozumel Island is of paramount importance for Mexico, because of the good state of its marine ecosystems, and as a touristic spot that attracts thousands of divers every day. Most studies about the local reefs have been devoted to those formations located inside the Cozumel Reefs National Park, in the southwest side of the island; however there are other important reefs that have received little attention. The objective of this paper was to conduct an analysis of zooxanthellate coral community structure in six sites of the eastern and northwestern coasts of Cozumel, and to compare them with the status of the reefs already under federal management. The results showed that there were no significant differences in coral cover, diversity, evenness and taxonomic distinctness of reefs inside and outside the protected area, a pattern that differed from that reported in previous studies. The homogeneity in the ecological structure may have resulted from the combined effects of differential human pressure (high in PNAC reefs, low outside of the park), and the high coral mortality caused in all areas by category 5 hurricanes “Emily” and “Wilma” in 2005. Considering these findings, we suggest that local authorities must allocate more effort dedicated to the conservation of reefs in the eastern coast of the island, as some of them (especially Hanan) are very well developed and house species of particular interest such as Acropora spp.