Fish communities and habitat structures were evaluated by underwater visual censuses a rocky location impacted by thermal discharge (I) and at two control locations, one in a Sargassum bed (C1) and the other in a rocky shore with higher structural complexity (C2). Habitat indicators and fish communities exhibited significant differences between the impacted and control locations, with the impacted one showing a significant decrease in fish species richness and diversity, as well as a decrease in benthic cover. At the I location, only 13 fish species were described, and the average water temperature was 32+/-0.4 degrees C, compared with 44 species at C1 (25.9+/-0.3 degrees C) and 33 species at C2 (24.6+/-0.2 degrees C). Significant differences in fish communities among locations were found by ANOSIM with Eucinostomus argenteus, Mugil sp. and Haemulon steindachneri typical of location I, while Abudefduf saxatilis, Stegastes fuscus and Malacoctenus delalandi were typical of the control locations. Our study shows that thermal pollution alters benthic cover and influences fish assemblages by altering composition and decreasing richness.