Phylogeographic analyses were conducted for the dung beetle Phelotrupes laevistriatus (Motschulsky, 1857) (Coleoptera: Geotrupidae), which exhibits geographic variation in flight-muscle condition. Beetles with well-developed flight muscles, and thus capable of flying, are distributed in middle and southern Japan, from northern Honshu to Kyushu, whereas those without detectable flight muscle are distributed in northern Japan, on northern Honshu and Hokkaido. To investigate the origin of the flight-muscle dimorphism in P. laevistriatus, we determined sequences of a 603-bp fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene for 258 individuals from 43 population samples. We constructed gene trees using the neighbor-joining method, maximum likelihood method, and maximum parsimony method and a haplotype network using the median-joining method. Six major clusters were recognized in each tree or network by these analyses. They occupied different ranges, being arranged from southwest to northeast as Clusters VI, V, IV, III, II, and I, with partial geographical overlaps between IV and III and between II and I. The beetles with well-developed muscles were included in all these clusters, whereas the beetles without detectable muscles were included in two northern clusters, i.e., Clusters I and II. The results suggest that the common ancestor of P. laevistriatus originally possessed flight ability and then diversified into regional clusters, after which the loss of flight muscles occurred in northern clusters, possibly in response to climatic conditions associated with increased latitude.