Mastigias jellyfish (“tako kurage”) have been reported throughout littoral Japan for over a century, historically identified by morphology alone as Mastigias papua. Molecular resolution of the genus in 2018 revealed three geographically structured clades and suggested Japanese populations instead belong to M. albipunctata, but subsequent morphology-only studies of Japanese specimens have continued to apply the M. papua designation, leaving species identity unresolved across much of the species’ Japanese range. Here, we use cytochrome c oxidase subunit I (COI), combining published GenBank sequences with two newly collected specimens from Okinawa, the southernmost extent reported in Japan. Maximum-likelihood and Bayesian phylogenetic reconstruction recovered three reciprocally monophyletic clades consistent with previous molecular work, with all Japanese sequences, from Sukumo Bay (Shikoku Island) to Okinawa Island, falling within the M. albipunctata clade. Morphological comparison against published diagnostic characters showed consistency with this identification. These results indicate that Mastigias populations in Japan are consistently identified as M. albipunctata, while highlighting the value of molecular analysis in tandem with morphology-based identification approaches.