<jats:title>Abstract</jats:title><jats:p><jats:italic>Dorcus montivagus</jats:italic> is a Japanese endemic stag beetle that feeds exclusively on dead beech wood, and its distribution is almost completely coincidental with that of beech forests. Japanese beech, <jats:italic>Fagus crenata</jats:italic>, is the dominant tree species of the cool‐temperate deciduous broad‐leaved forests in Japan. Historical changes in the distribution of beech forests due to Pleistocene climate change are expected to have also affected the phylogeographic structures of dependent beech‐feeding phytophagous insects. In this study, we elucidated the present phylogeographic structures of <jats:italic>D. montivagus</jats:italic> using molecular markers, and also compared them with the present geographic genetic structures of beech tress and the post‐glacial distribution as inferred by pollen fossil analyses. It was found that <jats:italic>D. montivagus</jats:italic> is largely differentiated into two phylogenetic clades: Clade I consisted of populations from Hokkaido, Honshu and Shikoku, and Clade II consisted only of Kyushu populations. Furthermore, the genetic diversity of the stag beetle showed a geographically declining gradient from south‐west to north‐east, consistent with the genetic variation observable in Japanese beech. Genetic differentiation between the Sea of Japan side and the Pacific Ocean side populations was also observed in both clades of the stag beetle. These results indicate a similar phylogeographic structure between the stag beetle and Japanese beech. Therefore, the distributional changes in Japanese beech correspondingly restricted the migratory dispersal of <jats:italic>D. montivagus</jats:italic>, and strongly influenced its phylogeographic structure.</jats:p>