Benthic assemblages of two Mediterranean submarine caves were compared. Species coverage and number of species were lower in internal (dark) communities than external. This feature was specially marked in the less illuminated cave. Ordination analyses performed on species coverage per community for each cave separately, distinguished several benthic communities from the outermost to the innermost zone of each cave. Cluster analyses on species coverage, taking into account all communities in both the caves, established similarities among communities: algal-dominated communities clustered according to the level of light received independently of the cave they inhabited, while animal-dominated communities were more similar within each cave than between the caves. Moreover, among the abiotic parameters measured irradiance was the only factor that clearly diminished from the entrance to the innermost zone in both the caves. In contrast, water movement and particulate organic matter varied differently in each cave. Results indicate that the different topography, depth and geographic location of the two caves determine water movement, light penetration and nutrient availability along the caves. These factors are responsible for determining species abundance and diversity, as well as species growth habit in each community.