An examination of the genetic population structure of Cobitis minamorii tokaiensis in central Honshu Japan, based on mitochondrial DNA nucleotide sequences in the cytochrome b region, revealed that the subspecies is subdivided into three regions (West-Shizuoka, Mie, and Aichi-Gifu) on the evidence of haplotype distribution and pairwise Φst among populations. However, the phylogenetic analyses indicated that the haplotypes in the three regions belong to the same haplotype group, suggesting that C. m. tokaiensis dispersed following the interconnection of paleo-river systems within relatively recent geological time, and subsequently differentiated in several areas. Because of its genetic characteristics, the three regions are important for conservation of the subspecies’ genetic diversity.
