The amphidromous goby Hypseleotris cyprinoides is the most widely distributed Hypseleotris species in the Indo-Western Pacific Ocean. Recently, the species has declined around Japan because of environmental destruction, overexploitation, water pollution and the effects of invasive fish species, and has been designated as an “endangered species in Japan”. Because captive breeding for the preservation of endangered species is considered an indispensable course of action in conservation biology, the Japanese Association of Zoos and Aquariums (JAZA) is currently attempting such for H. cyprinoides. Furthermore, there exists an urgent need for comprehensive studies on the genetic population structures and diversity levels of the species for the promotion of effective conservation and management activities. The present study examined the genetic population structure, genetic diversity and gene flow of H. cyprinoides from the Philippines to southern Japan, covering the Kuroshio Current region of the western North Pacific. Eight hundred and thirty-five bp of the mtDNA control region were analyzed in 140 specimens taken from three localities: Okinawajima Island and Ishigakijima Island, Ryukyu Archipelago, southern Japan and Luzon Island, Philippines. A total of 113 haplotypes were detected, four to eight shared haplotypes occurring at all localities, which had high levels of genetic diversity (range: h = 0.9930–0.9984; π = 0.0133–0.0153). AMOVA, pairwise FST, and Nm revealed high gene flow among the three localities, suggesting overall genetic homogeneity and a single shared gene pool, due to high dispersal ability during the oceanic larval stage and likely influence of the Kuroshio Current. Conservation and management directives should recognize the potential of these areas for sustainable recruitment of the species.
