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Species in Cymothoidae (Crustacea: Isopoda) are cosmopolitan parasite infesting marine, freshwater and brackish water fishes. In Cymothoidae, Anilocra and Nerocila species have an elongated juvenile stage called the aegathoid stage. A total of 831 Japanese halfbeaks Hyporhamphus sajori (Beloniformes: Hemiramphidae) were collected from 11 sites in Japan. The aegathoid stage was seen infesting a Japanese halfbeak collected from Osaki-Shimojima Island, Kure City, Hiroshima Prefecture, and identified as Anilocra clupei by DNA barcoding using the COI and 16S rRNA sequences. The morphology of this individual was also almost identical to the aegathoid stage of A. clupei in the previous study. The prevalence of the aegathoid stage of A. clupei on Japanese halfbeaks was very low at 0.12％ in all of Japan and 0.93％ in the coast of Osaki-Shimojima Island. Aegathoid stages of A. clupei may have lower host-specificity than adult females, and be able to infest more comprehensive species of fish, which may increase the survivability of the aegathoid stages. [ABSTRACT FROM AUTHOR]