In Japan, two subspecies of Scolopendra centipedes, S. subspinipes japonica and S. subspinipes mutilans are widely distributed. However, these two subspecies often coexist. S. s. mutilans grows to a lager body size than S. s. japonica and the former subspecies is dark red in head color whereas the latter is dark green. In the Izu Islands, central Japan, both subspecies were collected on four islands (Izu-Oshima, Niijima, Kouzushima, and Shikinajima), but only the subspecies S. s. japonica was confirmed to live on two islands (Miyakejima and Hachijojima). The body size of S. s. japonica was larger on allopatric islands than sympatric islands, suggesting that some character displacement occurs between these subspecies. Molecular phylogeographical analysis based on partial mitochondrial DNA sequences (16S rRNA and COI) showed that morphologically identified subspecies are completely separated into two groups throughout Japan. Therefore, mating is limited within each subspecies and two are sexually isolated good species. Populations in the Izu Islands, also including the Izu Peninsula population, have a unique haplotype group to this region; so that, the gene flow may be limited for long time within this region. On Hachijojima, however, the different haplotypes were detected from individuals obtained near some human habitation.