Arabis serrata (Brassicaceae), a perennial plant widely distributed along the Japanese Archipelago, occurs in various habitats: for example, limestone zones, serpentine barrens, volcanic soils, and roadsides. It likely survived by adapting to its surrounding environment, resulting in great morphological and ecological variation. In this study, we performed a phylogeographic analysis to examine past changes in the distribution of A.serrata following climate oscillations during the Pleistocene. To cover most of A.serrata's range, leaves were collected from eight to ten individuals randomly selected from each of 37 populations in the Japanese Archipelago. Two chloroplast noncoding regions of the samples were amplified and sequenced: trnT(GGU)-psbD and trnH(GUG)-psbA spacers. Twenty-five haplotypes were detected and distinguished by 31 substitutions. Four main haplotypes were observed in many populations distributed throughout the Japanese Archipelago. According to the genetic boundaries detected using the Monmonier algorithm, A.serrata is clustered into four groups, each including several populations: Hokkaido Island, northern mainland Honshu, central Japan, and western Japan. The boundaries, however, were not robust because all genetic parameters did not support the differentiation among groups. These results indicate the absence of an obvious geographic structure in the distribution of A.serrata, suggesting that this species has experienced a rapid range expansion in postglacial times.