Compared to their fossil counterparts, living brachiopods are investigated far less often, due to their occurrence in remote environments such as dark caves or deep environments. Due to the scarcity of studies targeting in situ brachiopods’ populations, large-scale information on their distribution and ecological preferences is still lacking, especially on hardgrounds. The extensive employment of remotely operated vehicles (ROVs), however, has opened up the chance to better explore this taxon’s diversity and ecology in the mesophotic and bathyal zones. The analysis of over 600 h of video footage collected from 624 sites, from 40 m to 1825 m, located along the Ligurian and Tyrrhenian coasts of Italy and the Sicily Channel, allowed for a large-scale investigation. The four identified species, Novocrania anomala, Gryphus vitreus, Megerlia truncata and Terebratulina retusa, emerged as common macrofaunal components of the explored habitats, especially between 150 m and 250 m, with high occurrences in the northern areas, especially on offshore seamounts. All species can form dense aggregations of individuals, with M. truncata showing the densest populations on steep rocky terraces (up to 773 individuals m−2). Except for G. vitreus, the only species also recorded on soft bottoms, the others were found exclusively on hardgrounds, with N. anomala showing a peculiar ability to exploit anthropogenic substrates such as terracotta amphorae. No stable species-specific associations were noted, even if numerous species were frequently observed together. Although brachiopods do not show the conspicuous tridimensionality of large filter-feeders, their substrate occupancy and their role in pelagic–benthic processes support their importance in deep-sea Mediterranean ecosystems.