Precise taxonomic assignment of species is important for monitoring biodiversity in given habitats. This is especially true in freshwaters, where biodiversity is facing a number of threats. Cyclops kikuchii Smirnov, 1932 is a freshwater copepod species which was initially described based on specimens collected in Japan. Its morphological characteristics are very similar to those of the closely related Palearctic species Cyclops vicinus Uljanin, 1875. At first, C. kikuchii was described as a subspecies of C. vicinus (as C. vicinus kikuchii) then, its taxonomic position changed to a valid species. However, most illustrated guides on Japanese freshwater zooplankton include only C. vicinus as a valid taxon in Japan, and thus ignore C. kikuchii without mentioning the reason. Conversely, the latest monograph of Japanese freshwater copepods includes only C. kikuchii as a valid taxon, and thus ignores C. vicinus without any justifications. As such, the nomenclature of Japanese C.“kikuchii/vicinus” is currently confusing. The present study examines whether Japanese C. “kikuchii/vicinus” represent both or either of the species using molecular phylogenetics and morphological inspections. Relationships between the examined Japanese taxa and their European closest relatives are also discussed.