Common acorn barnacles of the genus Tetraclita exhibit high levels of morphological variations that have led to taxonomic confusion. In East Asia, Tetraclita japonica (Pilsbry, 1916) occurs in grey or purple forms while Tetraclita formosana (Hiro, 1939) is pink. However, recent studies revealed that the two taxa do not exhibit variations in the mitochondrial COI and control region sequences, suggesting that their species status is questionable and whether they should be treated as species, subspecies or color morphotypes is equivocal. In the present study, we found no significant genetic differentiation between T. formosana and T. japonica in the highly polymorphic control region and the two taxa also share common nuclear ITS1 genotypes. This suggests there is no evidence for reproductive isolation between T. japonica and T. formosana. The two taxa share similar arthropodal and opercular morphologies; the only difference between them is in the color of the parietes. The purple and grey forms of T. japonica co-exist in high abundance in Honshu, Japan. On the geographical scale, T. japonica dominates the shores in Honshu, Japan, and along the coast of southern China whereas it is very rare in Taiwan and Okinawa. In contrast, T. formosana (pink) is very abundant in Taiwan and Okinawa but absent from southern China and rare in Honshu, Japan. We interpret the nearly allopatric distribution, phenotypic differences in parietes color and insignificant genetic differences between T. japonica and T. formosana as indicative of the subspecies status of the taxa, namely Tetraclita japonica japonica and Tetraclita japonica formosana.