The oriental weather loach Misgurnus anguillicaudatus (Teleostei: Cobitidae) inhabits the waters of East Asia including Japanese Islands. The Japanese population of M. anguillicaudatus includes two major mitochondrial DNA (mtDNA) clades, but their evolutionary origin is unknown. In this study, we conducted phylogeographic analyses of M. anguillicaudatus that were based on mtDNA cytochrome b sequences to clarify the evolutionary origin of the two distinct mtDNA clades. This newly obtained data were integrated with the mtDNA sequence data obtained in previous studies and reanalysed. The results showed that one major clade originated because of mtDNA introgression from a loach of the genus Cobitis. The geographic range of the populations carrying non-introgressed mtDNA tended to be limited to the peripheral areas of the Japanese Islands, whereas the range of the populations carrying introgressed mtDNA was spread over wide regions of the Japanese Islands. These distribution and divergence patterns suggested that M. anguillicaudatus populations carrying introgressed mtDNA have spread and replaced the range of populations carrying non-introgressed mtDNA.