The salamander Hynobius yatsui from southwestern Japan was formerly regarded as a small-sized group of H. naevius, but has recently been resurrected as a distinct species. We investigated the phylogeography of H. yatsui from Kyushu Island using partial sequences of the mitochondrial cytochrome b gene. We detected 49 haplotypes in 181 individuals from 24 localities covering the entire geographic distribution of this species on Kyushu. These haplotypes were grouped into two lineages, a northern lineage from northern and central regions, and a southern lineage from the southern region; no haplotypes were shared between the lineages. We surmise that the divergence of the two lineages was induced by volcanic activity that started in the Beppu-Shimabara Graben, between the areas occupied by these two lineages. From the results of a nested clade phylogeographical analysis, we surmise that the high intrapopulation genetic variation observed in the non-volcanic Kyushu Mountains was generated by alternation of contiguous range expansion or long-distance dispersal, and isolation. The current distribution and the observed complicated genetic structures of H. yatsui in Kyushu seem to have been affected first by volcanic activities since the late Pliocene, but subsequent climatic oscillations during the Pleistocene may also have some effects, although it is impossible at this time to differentiate the effects of these two factors.