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Iquius nipponicus Jordan was described on the basis of a single specimen from the Miocene of Iki Island, Nagasaki, Japan, and was tentatively assigned to the family Clupeidae. The holotype consists of the anterior portion of the body (lacking the anal and caudal fins and most of the caudal vertebrae), and is re-examined. The species is re-described based on additional specimens from the type locality. This species possesses an extremely stout third dorsal spine-like fin ray with a smooth posterior edge, an expanded anterior portion of the maxilla covering approximately half of the bone, 13 branched anal fin rays, and 22 abdominal and 16 caudal vertebrae. A phylogenetic study using the character matrix from a previous study suggests that the species forms a clade with xenocyprinins, but it differs from xenocyprinins in the form of the maxilla and the dentary and the numbers of branched anal fin rays and vertebrae. The present study concludes that the genus Iquius does not belong to the family Clupeidae. Iquius is a distinct and valid genus that is closely related to cultrins and xenocyprinins of the family Cyprinidae. [ABSTRACT FROM AUTHOR]