Although dams influence fish assemblages through fragmentation and flow regime alteration, the influence at a broad spatial scale had been poorly evaluated. Thus, we compared freshwater fish assemblages between upstream and downstream of dams in 67 rivers of Japan using Jaccard similarity index. Effects of dams on differences between fish assemblages in upstream and downstream are hypothesized to vary with the latitude. At first, the fish assemblages may be dissimilar in the northern regions compared with the southern regions because the northern regions have more migratory fishes that are sensitive to the fragmentation by dams. Alternatively, the fish assemblages may be dissimilar in the southern regions compared with the northern regions because flood controls by dams may have greater impacts on fish assemblages in the southern regions, which have more variations of precipitation. In this study, we tested the two hypotheses. However, the similarity did not reveal a distinct pattern along the latitude. The result suggests that the fish assemblages should be influenced by combined factors rather than a single factor.