Aim:The two additive components of β-diversity, namely turnover and nestedness, reflect the two basic mechanisms underlying the overall change in species identities across the landscape, the replacement of species or their loss, respectively.Analogously, functional turnover and nestedness express the replacement or loss of functional traits associated with variations in community composition. However, the extent to which patterns of compositional and functional nestedness and turnover may overlap, or diverge, is still uncertain in marine environments. Here, patterns of turnover and nestedness were quantified in marine benthic assemblages in order to assess their relative contribution to spatial patterns of compositional and functional -diversity. Location: Mediterranean Sea, NE Ionian Sea, Ionian Archipelago. Methods: In this study, we investigated patterns of dissimilarity in species and functional trait composition in subtidal macrobenthic assemblages from Mediterranean islands in order to quantify compositional and functional β-diversity among islands, determine the relative contributions of turnover and nestedness, and compare β-diversity patterns occurring in shallow and deeper reefs. Results: We found a complex relationship between functional and compositional β-diversity at varying depth. At 5 m, species and functional trait dissimilarity largely overlapped, with turnover being the dominant component in both cases. At 15 m, compositional β-diversity was mostly due to turnover, with a negligible contribution of nestedness, whereas the opposite occurred for functional β-diversity. Partitioning β-diversity components revealed this discrepancy and the presence of functional hotspots, which would remain unnoticed analysing the overall compositional and functional β-diversity. Main conclusions: Our findings may have profound implications for the optimization of conservation planning, stressing the need for assessing habitat-dependent idiosyncrasies in components of functional and compositional β-diversity for a more B I OS K E TCH Stanislao Bevilacqua and Antonio Terlizzi are marine biologists working at the University of Trieste as senior researcher in ecology and full professor in zoology, respectively. Their research activities focus on, but are not limited to, marine biodiversity conservation, human-driven changes to marine communities and ecosystems, and spatio-temporal patterns of species distribution. S U PP O RTI N G I N FO R M ATI O N Additional supporting information may be found online in the Supporting Information section. How to cite this article: Bevilacqua S, Terlizzi A. Nestedness and turnover unveil inverse spatial patterns of compositional and functional β-diversity at varying depth in marine benthos. Divers Distrib. 2020;26:743-757. https ://doi.