It has been claimed that most squid species in the genus Onykia may be immature stages of species in the genus Moroteuthis. To evaluate the generic status of Moroteuthis and Onykia and to identify paralarvae collected in northern Hawaiian waters, we performed morphological investigation and nucleotide sequence analysis of the mitochondrial cytochrome oxidase I (COI) gene. Of 42 Onykia paralarvae (1.8–8.5 mm dorsal mantle length, DML) examined, 41 had a nucleotide sequence identical to that of M. robusta and one (designated Onykia sp. A) could not be assigned to any known Moroteuthis species. Nucleotide sequence diversity estimates based on Kimura's two-parameter distances between Onykia sp. A and Moroteuthis spp. (0.109–0.150) fell well within the range of congeneric species, suggesting that Onykia sp. A is a member of the genus Moroteuthis. Molecular data supported the conclusion that the genus Moroteuthis is a junior synonym of the genus Onykia. Morphological investigation revealed that paralarvae of O. robusta (= M. robusta) <4.0 mm DML were distinct from other Onykia paralarvae in the chromatophore pattern on the mantle. The key characters for distinguishing O. robusta paralarvae from Onykia sp. A were the number and arrangement of chromatophores on the funnel.