The distribution of molluscan species at six cold-seep sites at between 5291 and 6290 m on the landward slope of the Japan Trench was studied using the crewed submersible Shinkai 6500 and the ROV Kaiko. At least four species of bivalve (Acharax johnsoni, Calyptogena phaseoliformis, C. fossajaponica and Parathyasira kaireiae) and three species of gastropod (Retiskenea diploura, Provanna abyssalis, and Provanna shinkaiae) were determined to be endemic to chemosynthesis-based communities. Two gastropod species (Bayerius arnoldi and Admete tenuissima) were confirmed to be colonists in chemosynthesis-based communities. The molluscan assemblages were of differing composition at each site. The two dominant bivalves, C. phaseoliformis and C. fossajaponica, showed specific differences in their distributions. C. phaseoliformis was mainly associated with silt sediments, whereas C. fossajaponica dominated the aggregations on pebble substrates. However, in a single case of co-dominance by both Calyptogena species, almost all individuals were of small size. The small gastropod Retiskenea diploura was found in clusters on the shell surface of C. phaseoliformis and on the silt sediments within the aggregations. This is the first record of a species of the family Neomphalidae from a chemosynthesis-based community in Japanese waters. The Molluscan faunal assemblages of cold-seep communities in the Japan Trench are similar at the familial and generic levels to those of cold-seep communities in the eastern Pacific, especially the Aleutian Trench subduction zone.