Ikiculter chojabaruensis is described on the basis of three specimens from the Miocene of Iki Island, Nagasaki, Japan, as a new genus and species of the family Cyprinidae. This new species possesses an elongate body, modified first unbranched fin ray of dorsal fin, extremely stout third dorsal spinelike fin ray with smooth posterior edge, apart tips of deeply forked basipterygium with a dorsal wing, elongated pterotic, smooth surface of opercle, large third vertebra twice as large as second one, 13 branched anal fin rays and 21 abdominal and 20 caudal vertebrae. A phylogenetic study using the character matrix of a previous study suggests that the species is related to leuciscins phoxinins, Ecocarpia, Iquius, xenocyprinins and cultins and is probably a sister taxon to a clade of Iquius xenocyprinins and cultrins. An extinct group closely related to Recent cultrins and xenocyprinins existed in Miocene East Asia.