Precise taxonomic assignment of species is important for monitoring biodiversity in given habitats, especially in freshwaters where the biodiversity faces a number of threats. Cyclops kikuchii Smirnov, 1932 and Cyclops vicinus Uljanin, 1875 are two closely related freshwater cyclopoids widely distributed in Eurasia, yet they are confusingly described in the Japanese literature. Therefore, we examined whether "C. kikuchii/vicinus" sensu Japanese literature represents both or either of the species. 137 Japanese "C. kikuchii/vicinus" specimens were collected from 22 localities across Japan, and nuclear ITS-1 and mitochondrial 12S (mt12S) genes were sequenced. The ITS-1 phylogeny separated Japanese "C. kikuchii/vicinus" into two genetic groups; one was clustered with European C. kikuchii (labeled here CkikJPN) while the other was clustered with European C. vicinus (CvicJPN). Morphological analyses using terminal furcal setae' lengths revealed that CkikJPN and CvicJPN correspond to C. kikuchii and C. vicinus, respectively. The mt12S phylogeny showed that European C. kikuchii could be a distinct species from Japanese C. kikuchii as the degree of sequence differentiation was nearly at the interspecific level.