The present study deals with benthic community structures of mussel beds (Mytilus galloprovincialis) in the Sea of Marmara, including the canakkale and Istanbul Straits. The Sea of Marmara's mussel beds were mainly formed by small-sized mussel individuals (shell length < 4 cm). Macrobenthic species associated with the mussels support high diversity in the region, comprising 184 species belonging to 11 taxonomic groups. The annelids (38% of total number of species) were the most diverse group and arthropods (48% of total number of individuals) the most abundant. Motile species numerically dominated mussel beds at stations, while epibiont fauna were relatively low in terms of number of species and abundance. Five different species assemblages were identified in the region, which appeared to be mainly influenced by some biotic (e.g. mussel biomass, alien species) and abiotic (e.g. salinity) factors. The assemblages were mainly characterized by having high abundances of three crustacean (Jassa marmorata, Hyale schmidti and Melita palmata) and one polychaete (Platynereis dumerilii) species. Seven alien species were found at stations, of which the small-sized anthozoon Diadumene cincta accounted for 86% of total number of individuals of alien species.