Coralligenous formations represent one of the most complex and species-rich benthic habitats in the Mediterranean Sea, providing a wide variety of ecological niches for cryptic sponge communities. These assemblages, including boring and cavity-dwelling species, play a key role in bioerosion, carbonate turnover, and the maintenance of habitat structural complexity. In this study, cryptic sponge assemblages inhabiting coralligenous concretions were investigated at eight locations distributed along the Italian coastline, encompassing the Ligurian, Tyrrhenian, Adriatic, and Ionian Seas. Coralligenous blocks collected by SCUBA diving were sectioned and examined using stereomicroscopy coupled with image analysis. Sponge abundance was quantified as Sponge Occupied Surface (AOS), while the Void Area Fraction (%VAF) was measured to estimate the availability of internal microhabitats. A total of 121 sponge species were recorded. Marked differences were detected between coralligenous rims and banks, with rims characterized by higher internal porosity, greater sponge cover, and increased species richness. Among the investigated areas, Ligurian rims hosted the most extensive sponge occupation and the highest variability in community composition. In contrast, banks from southern Italy generally supported lower sponge abundance, likely reflecting the combined effects of sediment accumulation and competition with algal assemblages. The sponge communities from Tavolara (Tyrrhenian Sea) were clearly distinct from those of the other sites, suggesting an important influence of depth and habitat morphology on assemblage structure. Extrapolation of local AOS estimates to the regional distribution of coralligenous habitats indicated that cryptic sponges make a substantial contribution at the ecosystem scale, with the greatest overall extent estimated for Apulia due to its broad coralligenous coverage. These results underline the importance of internal habitat architecture in determining cryptic sponge diversity and support the inclusion of three-dimensional habitat features in future conservation and monitoring programs.