In the central Japan, three distinct color forms of a geotrupid beetle Phlotrupes auratus occur parapatrically: the indigo form is distributed on the Kii peninsula; the green form in the southern side of Lake Biwa; and the red form in the areas where the indigo and green forms are not found. To discuss the origin of the three color forms, we examined the gene flow among color forms based on 745 bp of mitochondrial CO I gene. Multi Dimensional Scaling (MDS) based on F_st and D_A values discriminated populations of red form in western side of Lake Biwa from all the other individuals. MDS based on F_st value also discriminated populations of red form in eastern side of Lake Biwa from the other different color forms. Furthermore, three populations of green form on the side of Lake Biwa were discriminated from the others on the side of Kii peninsula and indigo. However, pairwise F_st values were significant between a population on the side of Kii peninsula in green form and populations of indigo, despite insignificance among all populations of green. Average F_st between red and green on the side of Lake Biwa was not also significantly larger than between indigo and green on the side of Lake Biwa. Gene flow expected from these results fitted closely with the hypothesis that a green form was originated from a hybrid of indigo and red forms.