Multi-facet diversity indices have been increasingly widely used in conservation ecology but congruence analyses both on horizontal and vertical axes have not yet been explored. We investigated the vertical and horizontal distributions of and taxonomic (TD), functional(FD) and phylogenetic diversity (PD)in a three-dimensional structured ecosystem. We focused on the Mediterranean coralligenous assemblages which form complex structures both vertically and horizontally, and are considered as the most diverse and threatened communities of the Mediterranean Sea. Although comparable to tropical reef assemblages in terms of richness, biomass and production, coralligenous assemblages are less known and more rarely studied, in particular because of their location in deep waters. Our study covers the entire range of distribution of coralligenous habitats along the French Mediterranean coasts, representing the most complete database so far developed for this important ecosystem. To our knowledge, this is the first analysis of spatial diversity patterns of marine biodiversity on both horizontal and vertical scales. Our study revealed that taxonomic diversity differed from functional and phylogenetic diversity patterns at the station level, the latter two being strongly structured by depth, with shallower stations generally richer than deeper ones. Considering all stations, phylogenetic diversity was less congruent to taxonomic diversity (Pearson’s correlation of r = 0.48) but more congruent to functional diversity (r = 0.69) than randomly expected. Similar congruence patterns were revealed for stations deeper than 50 m (r = 0.44 and r = 0.84, respectively) but no significantly different congruence level than randomly expected was revealed among diversity facets for more shallow stations. Mean functional - and - diversity were lower than phylogenetic diversity and even lower than taxonomic - and -diversity for both vertical and horizontal scales. Low FD and PD values at both - and -diversity indicated functional and phylogenetic clustering. Community dissimilarities (-diversity) increased over depth especially in central and eastern part of the French Mediterranean littoral and in northern Corsica, indicating coralligenous vertical structure within these regions. Overall horizontal -diversity was higher within the 50–70 m depth belts. We conclude that taxonomic diversity alone is inadequate as a basis for setting conservation goals for this ecosystem and additional information, at least on phylogenetic diversity, is needed to preserve the ecosystem functioning and coralligenous evolutionary history. Our results highlight the necessity of considering different depth belts as a basis for regional scale conservation efforts. Current conservation approaches, such as the existing marine protected areas, are insufficientin preserving coralligenous habitats. The use of multi-facet indices should be considered, focusing on preserving local diversity patterns and compositional dissimilarities, both vertically and horizontally.