Habitat connectivity exerts a significant effect on the structure of biological communities. However, it is generally difficult to study such an effect while controlling for other specific components of habitat structure. Here, temperate fish assemblages were studied in artificial reefs in localities differing chiefly in connectivity among complex habitat patches. Total fish abundance and biomass were higher in localities with high habitat connectivity, while species evenness followed the opposite trend. In most cases, the assemblages can also be distinguished by composition and relative abundance of species, as well as multispecies variability. Species responses were related to specific ecological profiles. Small species and those with restricted mobility were associated with high habitat connectivity. By contrast, medium-sized, off-reef foragers and vagile species were associated with reef isolation. The abundance ratio between 2 representative families of both groups of species, labrids and sparids, confirmed this finding. The temporal consistency of the observed patterns was also studied. The assemblages differed between periods of the year in terms of species composition and relative abundances. Total fish abundance, number of species and evenness were higher during the cold period than the warm, due to the presence of transient species. The results highlight the importance of habitat connectivity for the conservation and management of Mediterranean reef fishes.