The physical habitat characteristics associated with spatial distribution patterns of the freshwater mussel Pronodularia japanensis, which is used for oviposition by the Tokyo bitterling Tanakia tanago, were investigated in a small stream within a Tokyo bitterling protected area. The distribution of the mussels was found to be in an under-dispersed, non-random spatial pattern. Mussel occurrence correlated negatively with sediment softness, and positively with flow velocity, while mussel abundance was associated negatively with sediment softness and positively with sediment type (particle size). Furthermore, mussels were scarce in riverbed areas with a lack of sediment. These correlations suggest that the population dynamics of mussels and Tokyo bitterling may be influenced by changes in stream sediment conditions. To conserve the symbiosis between Tokyo bitterlings and mussels, a suitable benthic environment is required.