The Mesoamerican coral reefs are suffering from numerous anthropogenic stresses that threaten the long-term survival of this biologically, economically and culturally important ecosystem. A major method used to conserve these reefs is the establishment of marine protected areas (MPAs), which limit fishing and human development in coral sites. Despite their extensive use, it is uncertain how effective marine protective areas are at conserving Mesoamerican coral reefs. Utila and Cayos Cochinos are two islands in the Mesoamerican reef system that provide an excellent opportunity to study the effects of establishing a MPA on Mesoamerican reefs. Cayos Cochinos has been enforced as a primarily no-take MPA since 2003, and Utila is a nearby dive centre with largely unregulated fishing and coastal development. Cayos Cochinos and Utila were analyzed for coral cover, macroalgae cover, benthic taxa composition and diversity to compare the coral reef health on both islands. The Cayos Cochinos MPA has increased soft and scleractinian cover and decreased algae cover compared to Utila. Cayos Cochinos reefs also have increased coral diversity compared to the Utila reefs. This supports the theory that establishing a MPA can increase the health of the coral reefs in the protected area. Three other sites in the Mesoamerican reef, Puerto Morelos, Banco Chinchorro and Xcalak, were also analyzed for coral cover, species diversity and species composition to determine if the reef communities in other areas of the Mesoamerican reefs are similar to Cayos Cochinos and Utila. This provides a good estimate as to the extent that the results from Cayos Cochinos and Utila can be extrapolated to the rest of the Mesoamerican reef.