Three species, Luciola unmunsana and L. papariensis, endemic to Korea and L. tsushimana, endemic to Japan, have been taxonomically controversial whether they are independent or a single species for a long time. Therefore, we examined genetic diversity and evolutionary history of these species as well as including the related congeners using COI gene sequences (DNA barcoding region). Interestingly, we found seven paraphyletic groups from three species: two paraphyletic groups from L. papariensis, three paraphyletic groups from L. unmunsana and two paraphyletic groups from L. tsushimana. Among them, the group III of L. unmunsana collected from Jeolla-do province has never been recognized in the previous studies. A molecular clock analysis indicated that the origin of the major lineages of L. unmunsana, L. papariensis and L. tsushimana occurred between ~5.62 to 3.16 Ma. The origin of the major lineages of the group II and III of L. unmunsana, the group II of L. papariensis and the three groups of L. tsushimana occurred in 3.49 Ma (4.45–2.51 Ma, 95% HPD), which is consistent with the final disconnection of Japan from Korean Peninsula. The subsequent divergences of these paraphyletic groups clearly showed they have undergone allopatric speciation associated with geologic events in Korea and the sea level changes between Korea and Japan.