The firefly subgenus Hotaria sensu lato of the genus Luciola currently includes four morphospecies: L. ( H.) parvula, L. ( H.) unmunsana, L ( H.) papariensis, and L. ( H.) tsushimana. The latter three are taxonomically controversial based on both morphological and molecular data. We examined the phylogenetic relationships and evolutionary history of the species and related congeners using partial COI gene sequences (DNA barcoding). Our phylogenetic analyses consistently supported the monophyly of Hotaria sensu lato, but did not resolve the generic rank. The two types of L. ( H.) parvula in Japan can be considered distinct species that arose by pseudocryptic speciation during the Miocene, with substantial genetic divergence (15.41%). Three morphospecies, L. ( H.) unmunsana, L ( H.) papariensis, and L. ( H.) tsushimana, split into several polyphyletic or paraphyletic groups, forming entangled species groups. They are considered an incipient group that is distinguishable genetically but not morphologically, with evidence for recent allopatric speciation events corresponding to geologic events and sea-level changes during the Pliocene and Pleistocene. Group III of L. ( H.) unmunsana collected from the Jeolla region is a new taxon.