Evaluating the response of coral assemblages to different disturbances is important because variations in species composition may have consequences for ecosystem functioning due to their different functional roles in coral reefs. This study evaluates changes in diversity, structure and composition of coral assemblages of the coral reefs of two national parks in the northern sector of the Mesoamerican Barrier Reef System spanning the period from 2006 to 2012, just after the impact of two hurricanes in the area. Coral assemblages in the Cancún National Park included fewer species and lower live coral coverage (<15%) than those recorded in Cozumel. In the Cancún National Park, the species with the highest coral cover was Porites astreoides (more than 40% relative cover), and no significant temporal changes were observed in live coral cover and species composition. On the other hand, in the Cozumel National Park the dominant species were Agaricia agaricites, Siderastrea siderea and Porites astreoides, and the coral reefs showed an increase in live coral cover from 16% in 2006 to 29% in 2012. The dynamics of coral assemblages differed between the two parks: while there is an apparent stability in the current composition of the Cancún reefs, the Cozumel reefs show an increase in the abundance of the aforementioned dominant species. However, it is possible that the population characteristics of the species that dominate the coral assemblages in both national parks, such as those of fast population growth and of small colony size, do not entirely fulfill the main function of accretion and habitat heterogeneity, and more research is therefore needed to test this hypothesis.