We surveyed the genetic structure of Hynobius nigrescens Stejneger, 1907, a lentic breeding salamander widespread throughout montane and lowland regions of northeastern Japan. We performed a mitochondrial DNA analysis to explore intraspecific genetic variation and infer the evolutionary population history of H. nigrescens. Complete 1141 bp sequences of the mitochondrial cytochrome b gene were studied for 134 adult and larval individuals collected from 62 localities, encompassing the known range of the species. Hynobius nigrescens proved to be monophyletic, including two major clades (Clade II from southwestern Hokuriku and Clade I from all other localities). The latter clade comprises four well-supported and geographically structured subclades, which show genetic distances smaller than those seen in the widely sympatric species Hynobius lichenatus. Results of population statistical analyses indicated that Clade II of the westernmost range of H. nigrescens seems to have maintained a constant population size, while Clade I from most of the northeastern species range shows a tendency of recent population expansion, which is evident in Subclades I-A from the northernmost range and I-B from southern Tohoku to northern Kanto and eastern Chubu. In contrast, Subclades I-C from northeastern Chubu and Sado Is. and I-D from northwestern Chubu to Hokuriku seem to have been relatively stable in population size. Hynobius nigrescens differs greatly from other salamander species from northeastern Japan in its much more recent periods of genetic differentiation and its pattern thereof, and is suggested to be a young faunal element in this region.