The genetic structures of animal populations are influenced by the difference in the dispersal patterns of the sexes. To reveal effects caused by different dispersal systems between sexes on genetic structure, we examined the differences in the distribution of mitochondrial DNA in Asian black bears and compared the relationship between genetic correlation coefficients and pairwise distances of the bears between sexes using microsatellite DNA. From sequences of 758 black bears from continuous populations, we examined sequence data for 326 samples carrying ten haplotypes that were distributed locally. The estimated pairwise rectilinear distances indicated that males tended to distribute around the inner edge of the observed area of the locally distributed haplotypes. Distribution range analysis showed that both the maximum and average ranges of males in eight locally distributed haplotypes were larger than those of females. We also performed spatial autocorrelation analysis using genotype data for microsatellite DNA from 50 bears for which samples were collected from hair-traps. The genetic correlation coefficients were significantly higher than expected within the 0–10-km-distance class for females and the 0–20-km-distance class for males. These results revealed that males expanded the haplotype distribution and mediated gene flow.