Biological invasions by non-indigenous populations are one of the most serious problems for the conservation of genetic resources in natural environments, due to the likelihood of such populations becoming established and negatively impacting the genetic integrity of indigenous populations through hybridization and introgression. In central Japan, freshwater fish populations have been isolated by the Ibuki-Suzuka mountains between the Ise Bay basin (Gifu, Mie and Aichi prefectures on the eastern side of the mountains) and Lake Biwa water system (Shiga, Kyoto, Osaka and other prefectures on the western side), subsequently becoming genetically divergent. On the other hand, nonindigenous populations of freshwater fishes have been introduced to the rivers of the Ise Bay basin as a consequence of transplantation of commercially important Ayu (Plecoglossus altivelis altivelis) being accompanied by other species from Lake Biwa. Because some serious genetic disturbance of some species has already been reported from the former system, it is necessary to clarify the magnitude of such invasions and introduce measures for the conservation of native populations. This study focused on Japanese dace, Tribolodon hakonensis, one of the most common local fishes, which exhibits genetic differentiation between the Ise Bay basin and Lake Biwa system populations. Due to the superficial similarity between Japanese dace and Ayu, a bycatch of the former has been transported with Ayu from Lake Biwa to the other areas. To understand the magnitude of invasions from Lake Biwa, the PCR-RFLP method was used to discriminate between indigenous and non-indigenous mitochondrial DNA (mtDNA) haplotypes of Japanese dace in Gifu Prefecture rivers of the Ise Bay basin. Non-indigenous mtDNA haplotypes (Lake Biwa types) were found to be highly abundant in dam reservoirs, while less so in rivers, suggesting that Lake Biwa dace more easily adapt to the lacustrine environment of dam reservoirs than to river environments.