ABSTRACT. Spatial variations of hermatypic coral assemblages were evaluated at five sites in Cayos Cochinos Archipelago, Honduras, in February 2008. Richness and coverage of corals and other benthic morpho-functional groups were estimated using 56 videotransects. Topographic complexity and depth were also measured by transect. Twenty-two coral taxa were recorded for Cayos Cochinos. Total species richness was similar (16 and 17 taxa) at all sites, whereas species richness by transect was different among sites (6-12 taxa). Shannon diversity showed weak differences among sites (1.46-2.13), whereas Pielou evenness was not different among sites. Simpson dominance was low with weak differences among sites (0.15-0.27). The total cover of hermatypic coral was 16.5% at Roatan Bank, 10.5% at Salamandinga, 9.7% at Punta Pelicanos, 7.6% at La Grupera, and 6.9% at Mariposales. The ANOSIM revealed assemblages of different corals between sites, except between La Grupera, Punta Pelicanos, and Salamandinga. The NMDS associated La Grupera, Punta Pelicanos, and Salamandinga given the greater contribution of Porites astreoides, Agaricia agaricites, and Montastraea annularis; whereas the NMDS differentiated Mariposales and Roatan Bank, which had more dissimilar assemblages with a greater predominance of Montastraea cavernosa, Agaricia agaricites, and Diploria labyrinthiformis. According to the BIO-ENV method, coral composition and abundance were correlated with the cover of articulated calcareous algae, sandy substrate, total hermatypic corals, rockycalcareous substrate, fleshy macroalgae, and hydrocorals. In general, the differences found in the coral assemblages of Cayos Cochinos could be due to geomorphological characteristics as well as the effects of human activities in the study area.