Data on species diversity and structure in coralligenous outcrops dominated by Corallium rubrum are lacking. A hierarchical sampling including 3 localities and 9 sites covering more than 400 km of rocky coasts in NW Mediterranean, was designed to characterize the spatial variability of structure, composition and diversity of perennial species inhabiting coralligenous outcrops. We estimated species/ taxa composition and abundance. Eight morpho-functional groups were defined according to their life span and growth to characterize the structural complexity of the outcrops. The species composition and structural complexity differed consistently across all spatial scales considered. The lowest and the highest variability were found among localities (separated by >200 km) and within sites (separated by 1–5 km), respectively supporting differences in diversity indices. The morpho-functional groups displayed a consistent spatial arrangement in terms of the number, size and shape of patches across study sites. These results contribute to filling the gap on the understanding of assemblage composition and structure and to build baselines to assess the response of this of this highly threatened habitat to anthropogenic disturbances.