Habitat fragmentation from natural or human-mediated causes is a common phenomenon in terrestrial and aquatic environments. In this study, the effects of varying the size of habitat patches on the abundance of benthic invertebrates inhabiting date mussel (Musculista senhousia) patches was studied at two different transition environments, the Goro Lagoon (Adriatic Sea) and the Padrongiano Delta (Tyrrhenian Sea). Benthic fauna responded to habitat patchiness in a complex manner that varied according to habitat type, taxon and animal body size (small: 0.5–2.0 mm; large >2 mm). Small invertebrates were mostly polychaetes, nemertea, amphipods and isopods. Large invertebrates were mostly large polychaetes, bivalves, gastropods and crabs. Invertebrate population size and diversity seemed to be maximized in landscapes that include both small and large patches of mussel beds ‘embedded’ in a continuous matrix. Musculista senhousia patches served as a critical refuge and foraging habitat for many species. Patchy and continuous areas may promote the persistence of organisms with different life histories, especially in environments like those studied where mussel patches represent the only structural refuge available.