A Japanese native bumblebee, Bombus ignitus, has recently been commercialized for crop pollination. To assess the risk of genetic disturbance of local bumblebee communities, despite the fact that B. ignitis is native, we analyzed a 1048-bp sequence of the cytochrome oxidase subunit 1 (CO1) region of mitochondrial DNA in B. ignitus specimens that were collected from various localities in Japan, China, and Korea. We detected 15 haplotypes, none of which were shared between Japanese and continental populations. Phylogenetic analyses confirmed that the Japanese populations constituted a distinct clade that is genetically divergent from the continental populations. The detection of a geographic pattern in the CO1 haplotype distribution within Japan suggests genetic differentiation among Japanese populations. These results indicate that the genetic endemism of B. ignitus should be taken into consideration before commercial colonies of this native bumblebee are distributed.