The genetic structure of the Japanese robin Luscinia akahige across its breeding range was investigated based on mitochondrial cytochrome b and a control region sequence to reveal the phylogeographic history of this species, which is endemic to the islands around Japan. We obtained the 2,230-bp combined sequences of 77 robins from eight locations and identified 33 haplotypes. Of these, two phylogenetic clades, Ak and Tn, were evident in both maximum-likelihood and Bayesian analyses. Clade Ak was found throughout the range, whereas clade Tn was endemic to the Izu Islands, resulting in the mixture of both clades at this location. These two mtDNA lineages were inferred to have originated in different refugia during the mid-Pleistocene glacial period, probably one in southwestern Japan and the other in the Izu Islands. The population in the Izu Islands has been described as an independent subspecies, tanensis, and is known to be distinguished phenotypically from the nominotypical akahige. Therefore, the distribution pattern of the two mtDNA lineages may be better explained by past introgression of mitochondrial DNA rather than by assuming continuous hybridization with immigrants from the mainland. Future nuclear DNA analysis is needed to evaluate the effect of this introgression event on the genetic bases of the current Izu Islands population. Within clade Ak, the haplotype distribution pattern was inferred to be primarily a result of contiguous range expansion, reflecting the history of both range and population expansion after the last glacial period, with some effects of allopatric fragmentation in its southwestern range.