The Ostrinia latipennis group contains two species, O. latipennis (Warren) and O. ovalipennis Ohno. These two species commonly utilize perennial knotweeds (Fallopia spp.) as their host plants, which are serious invasive weeds in Europe and North America. Ostrinia latipennis is widely distributed across north-east Asia including Japan whereas O. ovalipennis is restricted to north Japan (Hokkaido Is.) and highland areas of central Japan (Nagano Prefecture in Honshu Is.). To estimate the phylogenetic relatedness and geographical differentiation of the two species, mitochondrial COII gene sequences were determined for specimens covering their distribution ranges in Japan. The uncorrected sequence divergence between O. latipennis and O. ovalipennis was 0.6–0.7%, supporting a close relationship. According to the standard molecular clock proposed for arthropod mtDNA, the two species are speculated to have diverged about 0.3 Myr ago. A single COII gene haplotype was found in O. latipennis irrespective of collection locality. In contrast, two haplotypes were found in O. ovalipennis, and their frequencies were significantly different between the Hokkaido and Honshu populations. The patterns of geographical variation in the COII gene within the two species were in agreement with previously reported patterns of geographical differentiation in morphology of the two species in Japan. The present results support the hypothesis that gene flow among local populations of O. ovalipennis has been limited by geographical isolation.