In the Japanese main islands, two brook damselfly species are sympatrically distributed. One is highly endangered damselfly, Copera tokyoensis, Asahina, 1948, and the other is a congeneric common species, C. annulata (Selys, 1863). Mitochondrial gene genealogy reconstructed by the maximum likelihood method showed that they are not reciprocally monophyletic. These two congeneric species might have experienced mitochondrial introgressions possibly through hybridizations. The effect of hybridization against endangered species is generally poorly understood. Taxonomic uncertainty might also explain this situation because extremely dispersed pattern of the haplotype network could not be appeared by once or twice hybridization. Three closely located populations of C. tokyoensis in the Kanto district showed significant population differentiation. It might suggest the low dispersal tendency of this endangered species.