The biogeography of freshwater fishes in Japan was reviewed in terms of achievements and perspectives. In the last three decades, biogeographic studies have changed from earlier descriptions of the freshwater fish fauna, based on the Linnean classification system, to phylogenetic approaches using various molecular markers. Especially, the phylogeographic approach, which explores the formation of geographic distribution patterns of genealogical lineages within species, has become predominant. Analyses of genuine freshwater fishes have disclosed their speciation and dispersal patterns throughout temperate East Asia since the Neogene, along with the formation of the Japanese Archipelago. In particular, molecular clocks of mitochondrial DNA have played an important role in examinations of biogeographic relationships between the Japanese Archipelago and Chinese continent/Korean Peninsula, and vicariance by Fossa Magna in central Honshu Island. Patterns of range expansion through the sea and landlocking in coldtemperature euryhaline fishes have indicated their speciation and distribution dynamics under the fluctuating climatic conditions of the Plio-Pleistocene. Likewise, phylogeographic implications of unusual biological entities arising from interspecific hybridization or gynogenesis have been discussed. Nevertheless, despite the emphases given to some groups, the present knowledge of phylogeographic patterns of Japanese freshwater fishes is for the most part still insufficient for quantitative analyses of the overall history of the freshwater fish fauna and geographic regions of Japan. Improved research techniques and methodologies for the integration of findings from multiple taxa and/or genes are essential. Further, evolutionary formation of distributional ranges should be considered together with ecological biogeography, including the processes of local adaptation, interspecific interaction and extinction. Modern day disturbances of freshwater fish distributions, including fish transportation, are rapidly leading to artificial distribution patterns and extinctions. Exhaustive phylogeographic analyses should be necessary as a primary requirement for conserving freshwater fish biodiversity in Japan.
