ABSTRACT. – Stiphodon percnopterygionus (Gobiidae: Sicydiinae) is an amphidromous goby distributed mainly in the northwest Pacific Ocean, from Taiwan to the south of Japan. This study evaluated the population genetic structure of S. percnopterygionus using partial cytochrome oxydase I (COI). A total of 496 base pairs were sequenced for 88 individuals from six localities. Twenty-eight haplotypes were recovered. Diversity indices were h = 0.709 ± 0.003 and π = 0.05 ± 0.035 and are what is currently found for Sicydiinae gobies. All results lead to the conclusion that S. percnopterygionus population is expanding. Indeed, the haplotype network displayed a star-like pattern and the mismatch distribution analysis results indicate a recent demographic expansion. AMOVA results and the haplotype network indicate the absence of population structure within the distribution area sampled. The lack of population structure is probably due to the amphidromous life cycle. S. percnopterygionus larvae have a long marine dispersal phase (99 ± 16 days), allowing them to disperse far from their emission location, especially in the northwest Pacific Ocean, as larvae are probably transported by the Kuroshio Current.