Sponge assemblages play a significant role in the functioning of the Mediterranean benthic ecosystem. The main goal of this study was to investigate the diversity and distribution of poorly known sponge communities in the mesophotic and deep-sea substrates of the eastern Mediterranean Sea. More than 1500 sponge specimens belonging to 87 taxa were collected from 156 stations during experimental and commercial bottom trawling in the Aegean Sea and the eastern part of the Ionian ecoregion, at depths of between 10 and 800 m. A total of 79 sponge species were found in the Aegean and 40 species in the Ionian Sea. Eight of these species are included in lists of endangered and threatened species, two were newly recorded in the Aegean and six were first recorded in the east Ionian Sea. Both community structure and diversity differed between the two ecoregions. Species richness, biomass, abundance and diversity decreased with increasing depth, while different species dominated, in terms of biomass, abundance and frequency of appearance, in the two ecoregions and the separate depth zones. In contrast with previous investigations, which mostly examined shallow-water sponges, no clear resemblance patterns were observed among the north and south Aegean subareas, probably due to the homogeneity of the deep-sea habitats under investigation. This study, using sampling material from fish stock monitoring programs for the first time, contributed to our knowledge of the largely unknown eastern Mediterranean mesophotic and deep-sea sponge populations, which are subjected to intensive trawling activities.