To clarify the distribution during spawning and spawning habitat of Itasenpara bitterling (Acheilognathus longipinnis), one of the most endangered freshwater fish species in Japan, the habitats of mature individuals and freshwater mussels (Unio douglasiae nipponensis) were investigated in the Moo River (Himi City, Toyama Prefecture, Japan) in relation to environmental factors during the fall and winter seasons in 2010. Mussel density-influenced sex ratios of bitterling varied in the study area, males remaining in areas of high mussel density during spawning, while females frequented deeper feeding grounds until their eggs had matured.