We investigated natural populations of three Japanese native bumblebee species to determine the status of infestation by a tracheal mite, Locustacarus buchneri, which we had earlier detected in introduced commercial colonies of the European bumblebee, Bombus terrestris. We also investigated mite infestation in commercial colonies of a Japanese native species, B. ignitus, which are mass-produced in the Netherlands and reimported into Japan. We detected the mite in both natural and commercial colonies of the Japanese species. Comparison of 555 bp sequences of the mitochondrial DNA (mtDNA) cytochrome oxidase 1 (CO1) gene from the mite showed that there were seven haplotypes, on the basis of combinations of substitutions at eight sites in the gene. The haplotypes of the mites in the Japanese native bumblebees and the haplotypes of the mites in B. terrestris did not overlap; however, mtDNA of mites detected in the commercial colonies of B. ignitus possessed the same sequence as a European haplotype. These results indicate that transportation of bumblebee colonies will cause overseas migration of parasitic mites of different origins.