The genetic diversity of populations of the azuki bean beetle, Callosobruchus chinensis (Linnaeus) from natural, pre-harvest and post-harvest sites, was investigated to understand population structure and gene flow. A 522-bp fragment of the mitochondrial gene COI was sequenced for eight populations of C. chinensisfrom Japan, Korea and Taiwan collected from different habitats. Six haplotypes were detected, one of which, U1, occurred most frequently and widely. The following hypotheses were tested as a cause of the wide distribution of haplotype U1; (i) topographical separation (by national boundaries), (ii) host plant species, and (iii) habitat type (natural, pre-harvest crop, or post-harvest storage). Categorization of collection sites by country or by host species did not yield differences in the occurrence of haplotype U1, but habitat type did. Populations utilizing cultivated post-harvest hosts that were mass stored were highly likely to be the common haplotype, whereas host plants in natural habitats away from agriculture were utilized by populations with locally characteristic haplotypes. Sampling of commercial beans for quarantine and export purposes indicated that gene flow in C. chinensis was largely unidirectional into Japan at the present time.