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The diversity of benthic communities on continental shelves is tightly linked to the diversity of habitats. Therefore, considering seascape habitat composition can help to gain insights into the spatial variability of benthic communities and move away from single-habitats approaches. This perspective needs different analytical methods, such as network analysis that enable the study of complex ecological interactions. This work explores the relationships between habitat and benthic species diversity in the Menorca Channel (the Balearic Islands, western Mediterranean). The seascape in the study area is a mosaic of alternating biogenic and sandy habitats that increases the total benthic species richness. Of the 442 benthic species included in the analyses, 286 species are shared by the six habitats identified, contributing to ecological connectivity across the seascape; 73 generalist species inhabit all six habitats simultaneously, however, 156 species are specialists and are linked to a single habitat, particularly to biogenic habitats, which increases specialization and the vulnerability of the species to habitat fragmentation. The network approach shows a tight link between epibenthic species diversity and the distribution of habitats over the continental shelf, providing essential information for optimal conservation strategies that move from a focus on protecting the most sensitive habitats to marine conservation schemes that encompass a diversity of habitats. Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. This work was funded by EU H2020 MaCoBioS (Grant Number 869710) and the original data was produced under LIFE + INDEMARES project: ‘‘Inventario y designación de la Red Natura 2000 en área marinas del Estado español’’. SdJ is supported by a Ramon y Cajal postdoctoral grant funded by the Ministry of Science and Innovation (Plan Estatal I + D + I, 2017- 2020; grant no. RyC2020-029062-I). AO was funded by the General Directorate for University Policy and Research of the Government of the Balearic Islands with a “Vicenç Mut” award Grant PD/002/2020. JM was the INDEMARES project coordinator in the Menorca Channel for the period 2009–2014.

28 pages, 6 figures, 6 tables, supplementary material in https://doi.org/10.1007/s10531-011-0210-1, Menorca Channel (Balearic Islands, western Mediterranean) comprises 98,700 Ha of continental shelf. It has been proposed to include this area in the Natura 2000 network due to the wide range of species and habitats of high conservation value found here, such as Posidonia oceanica meadows and maërl and coralligenous beds. This study aimed to establish a scientific basis for managing and protecting the continental shelf bottoms in Menorca Channel. Sampling was carried out with side-scan sonar, beam trawls, box corers, a remote-operated vehicle and an underwater drop camera. The information collected was used to map the habitat distribution between 50 and 100 m depth, as well as make an inventory and describe the spatial patterns of both the specific and functional diversity. A total of 636 species was recorded in a mosaic of habitats in which Corallinacea calcareous algae and other soft red algae (Osmundaria volubilis and Peyssonnelia spp.) were the most abundant groups. Hotspots of specific and functional diversity were located in areas with high habitat heterogeneity and complexity. Protection of Menorca Channel should not only include the habitats and species in the European directives, but also the habitats that are not currently protected, such as O. volubilis and Peyssonnelia beds, due to their biogeographical and ecological interest and their contribution to the biodiversity of shelf bottoms in the Mediterranean Sea. © 2012 Springer Science+Business Media B.V., The study was financed by the Conselleria d’Agricultura i Pesca of the Government of the Balearic Islands within the Canal Project and in the framework of LIFE+ INDEMARES project: ‘‘Inventario y designación de la Red Natura 2000 en áreas marinas del Estado español’’. Sonography was carried out by Tecmarin 1990 SL and financed by the MarViva Foundation