Population genetic analyses were conducted for the flightless beetle Silpha perforata in northern Japan to evaluate effects of straits as dispersal barriers. In all, 19 populations on the Hokkaido mainland and one population on each of seven adjacent islands were included in the study. Based on partial sequences (853 bp) of the mitochondrial ND2 gene from 365 individuals, we calculated haplotype diversity (h), nucleotide diversity (π), Tajima's D, and Fu's F_s statistics for each population. The genetic distance d_A and fixation index F_ST were then estimated between populations, excluding two mainland and two island populations with small sample sizes. The results showed that four island populations (Rebun, Rishiri, Yagishiri, and Teuri) were genetically diverged and isolated from mainland populations, including the closest ones, consistent with the assumption that the straits separating these islands from the mainland have functioned as strong barriers against beetle dispersal. However, some factors other than sea barriers may have resulted in the observed divergence of these island populations, since the straits might be too young to permit such divergence (all are estimated to have been finally established approximately 11,000 to 13,000 years BP). On the other hand, the population on Okushiri Island showed little genetic divergence from the nearest mainland population, suggesting current overseas dispersal across the strait (estimated to have been formed more than 200,000 years BP). The present study thus demonstrated that the effects of straits on dispersal can be diverse, even for species of terrestrial invertebrates with limited dispersal ability.