Genetic characteristics of the Japanese torrent catfish Liobagrus reinii in the Miya River and neighboring drainages were investigated, using mtDNA and eight microsatellite (MS) markers, to evaluate the effects of man-made river structures on the distribution and genetic structure of the species. A total of 23 mtDNA haplotypes were detected, forming a star-like haplotype network, in which the population in the upper reaches (URM) formed a unique group. Many populations in tributaries of the middlelower reaches (MLRM) included unique haplotypes, although they shared a common haplotype located at the center of the network. MS markers indicated that genetic diversity tended to decrease upstream in the tributaries, coupled with a decline in effective population size and the existence of genetic bottlenecks. These phenomena were especially evident in tributaries isolated with weirs or dams. The fixation index RST, the values of which were smaller than FST, indicated isolation by distance (Mantel test), genetic differentiation among populations having occurred in recent years. Although a Bayesian-based assignment test showed unique clusters in the populations of isolated tributaries, including the URM population, many MLRM populations shared an admixture of multiple clusters, probably resulting from the dispersal of L. reinii. These results indicated that L. reinii in the Miya River included two conservation units, in the upper and middle-lower reaches, respectively. Man-made river structures seem to have caused fragmentation of the distribution of the species, resulting in small tributary populations suffering from genetic deterioration. In drainages neighboring the Miya River, the Isezi River population of L. reinii seems to be indigenous, owing to unique genetic characteristics in mtDNA and MS, whereas the sharing of genetic characteristics with the URM population of the Miya River indicated that the Akaba River population is likely to have been introduced from the Miyagawa Reservoir.
