To clarify the taxonomic status of the Burmoniscus ocellatus complex in Japan, we carried out morphological observations and phylogenetic analyses of specimens collected from Yonagunijima, Iriomotejima, Ishigakijima, and Miyakojima Islands of the southern Ryukyus and from Okinawajima Island of the central Ryukyus in southwestern Japan. Observations of the holotypes of Aphiloscia iriomotensis (Nunomura, 1986), Ap. ishigakiensis (Nunomura, 1986), and Ap. yonakuniensis (Nunomura, 1986), in addition to the specimens newly collected from the five islands, indicated that these specimens belong to the genus Burmoniscus. Analyses of five morphological characters of 268 specimens collected from the five islands showed that the body size of Okinawajima specimens is distinctly smaller than those of the specimens from the southern Ryukyus. The ranges of the five morphological characters tended to overlap among the specimens from Yonagunijima, Iriomotejima, Ishigakijima and Miyakojima Islands; these morphological characters were congruent with those of 6. ocellatus (Verhoeff, 1928). The phylogenetic analyses were based on three regions of mitochondrial DNA—COI, 12S rRNA, and 16S rRNA—and indicated that the specimens collected from the southern Ryukyus constitute a monophyletic group, which is clearly distinct from the clade composed of the Okinawajima specimens. These results strongly suggest that Ap. iriomotensis, Ap. ishigakiensis, and Ap. yonakuniensis are synonymous with B. ocellatus, a species widely distributed in the southern Ryukyus. On the other hand, the species from Okinawajima Island in the central Ryukyus is considered to be an undescribed Burmoniscus species, which is closely related to but clearly distinct from S. ocellatus.