Fish assemblages associated with shallow rocky bottoms along the coast of Cape Milazzo were investigated within three selected habitats, each represented by a different degree of complexity and namely vermetid reef (VR), rocky-algal reef (RR) and boulder and pebbles (BP). The area, located along the northern coast of Sicily (southern Tyrrhenian Sea) was studied by using a non-destructive diver visual census methodology evaluating species composition and abundance. A total of 39 fish taxa belonging to 15 families were recorded over the three habitats investigated. Multivariate and univariate approaches detected significant differences among the three habitats. These differences were either in fish assemblage structure, in the assemblage parameters or in the abundances of some common species. A multidimensional scaling performed on the entire fish density data set showed distinct groupings for the three habitats. The highest values of mean species richness (S), diversity (H′), evenness (J) and density (N) occurred over the more complex habitat, represented by VR, than over rocky-algal reef habitat or BP. Different habitat preferences were evidenced for several fish species. Diplodus sargus, Serranus scriba, Tripterygion tripteronotus, T. delaisi and T. melanurus were significantly more abundant over VR whereas Thalassoma pavo and Symphodus tinca were more abundant both over VR and BP habitats. Statistical comparison did not detect habitat preferences in Symphodus roissali, Oblada melanura, Diplodus vulgaris and Sarpa salpa. As far as the size is concerned, small, medium and large-sized specimens of D. sargus and only large-sized individuals of D. vulgaris were significantly more abundant over the VR habitat side than over the other two. These results suggest that differences in assemblage parameters are related to habitat structure. Greater habitat complexity means greater surface available, thus providing additional resources for adults and juveniles of many species: food, cavities, caves and then new niches, refuges from predation, from artisan fishery nets, as well as resting or mating sites, boosting the total number of individuals and species. The results of this study highlight the importance of VR in sustaining the biodiversity of fish assemblages and emphasize the need for their careful management in an area already proposed as a Site of Community Interest.