Abstract: Tetraclita japonica and T. formosana are common intertidal barnacles with similar morphology, which leads to uncertainty in their species status. In the present study, we try to elucidate the taxonomic status of the two taxa using morphology and mitochondrial control region and cytochrome c oxidase subunit I (COI) sequences of the barnacles in their distribution range. The two taxa were found to be morphologically similar; a diagnostic difference between them was only observed in the colour of the parietes and opercular plates. Little genetic differentiation was detected in the control region and COI (ΦCT < 0.025 for both markers) between two taxa, but differentiation was found between the southern (Taiwan and Hong Kong) and northern (Japan) populations of T. japonica/T. formosana, which might be the result of isolation by distance and upwelling in summer. Our data suggest that the two presently recognized species probably represent two colour morphotypes of the same species exhibiting different geographical distribution. T. japonica is abundant in Japan and southeast coast of China, whereas T. formosana is only abundant in Taiwan. The heterogeneous environment might exert a divergent selection pressure leading to asymmetric distribution of the two colour morphotypes. The different colours might be a result of either phenotypic plasticity adaptive to environmental variables or genetic hitchhiking of local adaptive genotypes.