River-crossing structures such as dam and weir cause fragmentation of aquatic habitats, which often prevents migration of aquatic fauna. In this study we evaluated such effect of fragmentation on probability of occurrence of freshwater fishes in several sections of Sagami River, Japan. Logistic-regression model describing the relation of habitat properties to presence/absence of each 41 fish species was statistically fitted to their distribution monitored from 1993 to 2005. The model considered six habitat properties of each section: basin area, longitudinal slope, isolation period, river width, upstream connection and downstream connection. As results, different habitat properties were selected for the model of each species and the correctly predicted ratio was over 75% for 28 species. These models imply the effect of fragmentation on fish distribution in the Sagami River and can be applied in several ways for river environment management.