Dark spots disease (DSD) is a relatively new coral disease that has become one of the most prevalent afflictions in the Caribbean Sea. To partially characterize bacterial communities associated with DSD, carbon utilization patterns of bacterial strains isolated from the surface mucopolysaccharide layers of healthy and DSD-affected Montastraea annularis, Montastraea faveolata, and Siderastrea siderea were compared with each other and with bacterial strains isolated from the water column by using cluster analysis. Differences between healthy and diseased corals were found and were greatest for M. annularis than for the other species. A metabolic group of bacteria similar to Vibrio carchariae was found to be unique to diseased samples. Inoculation experiments on healthy corals did not result in the development of disease signs. However, our results support the hypothesis that stress (in this case disease) alters the normal microbiota in the coral surface mucopolysaccaride layers. Studies are continuing to determine the pathogenic agent(s) responsible for DSD.