The hierarchical structure of areas of endemicity of freshwater fishes in the Japanese Archipelago was analyzed using parsimony analysis of endemicity (PAE) and its modification. Supporting the results of previous studies, the present analysis, which includes species, subspecies, intraspecific monophyletic lineages, and/or hypothetical ancestors, revealed the uniqueness of the local ichthyofauna in northeastern Hokkaido, large changes in ichthyofauna across the Fossa Magna region, central Honshu, and some additional new patterns. A split network analysis was used to represent the complex relationships among local faunas in the archipelago and also in East Asian regions. Artificially disturbed fish faunas have recently lost part of their original endemic areas, producing a remarkable “homogenization” among local faunas (+9.0% in Jaccard’s similarity coefficient). The majority of this homogenization can be explained by introduction of domestic species (+8.6%), especially from Lake Biwa, the largest lake in Japan.