Phylogenetic relationships were inferred for populations of the Ryukyu five-lined skink Plestiodon marginatus, a species showing an extraordinary distribution across the Tokara Tectonic Strait. Phylogenetic analyses of 809 base positions of the mitochondrial 12S and 16S rRNA genes supported collective divergence of the southern Tokara and northern Amami populations, which have been classified as P. m. oshimensis. A population from Nakanoshima, an island of the Tokara Group north of the Tokara Tectonic Strait, has the closest affinity with the Okinawajima population of P. m. marginatus rather than with the geographically closer southern Tokara and northern Amami populations. This result is concordant with that of a recent allozyme study and suggests an origin of the Nakanoshima population through long-distance dispersal from the Okinawa Island Group. Also, our results strongly suggest a closer relationship of a population of P. m. oshimensis from Okinoerabujima, a southern island of the Amami Group, with P. m. marginatus from Okinawajima than with the “consubspecific” southern Tokara and northern Amami populations. Both Nakanoshima and Okinoerabujima populations are usually referred to as P. m. oshimensis, and therefore our results indicate nonmonophyly of P. m. oshimensis in the current taxonomic arrangement.