Male brown bears (Ursus arctos) generally disperse over longer distances than females, which have conservative habitats around their natal areas. Our previous study indicated that the distributions of mitochondrial DNA (mtDNA) subhaplotypes in females were allopatric in the southern Akan—Shiranuka region of eastern Hokkaido. Dispersal of males from their natal area to another natal area is easily detected from the allopatric distributions of two of the mtDNA subhaplotypes of female bears (HB02a and HB13b). Here, to investigate the effectiveness of gene flow and dispersal of male bears between two natal areas, we assessed the genetic diversity and kinship of 132 brown bears from 1996 and 2008 in this area by analyzing the polymorphisms of mtDNA and microsatellite DNA. Parentage testing revealed that there were 48 potential father—offspring pairs, nine potential mother—offspring pairs, and four potential parent—offspring trios. Among 33 of the 48 father—offspring pairs, the mtDNA subhaplotypes differed between father and offspring, suggesting that these potential fathers moved from one natal area to the other and had reproductive success. The results show that effective dispersal of male bears has maintained the genetic diversity and gene flow between the two natal areas.