Disturbances that result in the mass mortality of reef-building corals are changing the appearance of reefs worldwide. Many reefs are transitioning away from scleractinian-coral-dominated assemblages to benthic communities composed primarily of non-scleractinian taxa. This study evaluated recovery patterns of reef communities in the Florida Keys following the mortality associated with the 1997/1998 El Niño. We examined temporal trends among the 5 most spatially abundant reef taxa and stony coral species from 1999 to 2009 at 3 spatial scales, and applied a Principal Coordinate Analysis (PCoA) to determine whether changes in their cover resulted in a shift in community structure. Trends of decreasing stony coral cover were not identified Keys-wide between 1999 and 2009, but 2 of the 3 habitats examined—shallow and deep forereefs—did show a significant decline in cover. Concomitantly, octocoral cover significantly increased Keys-wide and in all 3 habitats. The transition to octocorals was most evident on shallow forereefs, where octocoral cover significantly increased at 9 of 12 reefs and overwhelmingly influenced the PCoA. On deep forereefs, octocoral and sponge cover did significantly increase, but did not impart a clearly defined shift in community structure like that observed on shallow forereefs. Community composition at patch reefs was relatively consistent during the study, but the increase in octocoral cover may accelerate further following a cold-water mortality event in 2010. These results demonstrate that octocorals are emerging as the predominant benthic taxa in the Florida Keys. Although the transition to octocorals may have started long ago, their apparent resilience to present-day stressors will likely allow this shift to continue into the foreseeable future.