The genus Helice is comprised of four species, H. formosensis, H. latimera, H. tientsinensis, and H. tridens. A recent molecular analysis identified H. formosensis and H. tientsinensis as junior synonyms of H. latimera. We used three mitochondrial and two nuclear genes to further delineate species boundaries in Helice and to add to knowledge of the historical biogeography of the genus. The molecular data revealed deep divergences between the H. formosensis-latimera-tientsinensis complex and H. tridens. Clear genetic separations with incomplete lineage sorting and convincing morphological divergences were detected among H. formosensis, H. latimera, and H. tientsinensis, and a coalescence analysis revealed negligible gene flow among these species, except for weak unidirectional gene flow from H. formosensis to H. latimera. The estimated divergence time of 1.42–1.92 Ma between the H. formosensis-latimera-tientsinensis complex and H. tridens is consistent with the opening of the Tsushima/Korea Strait (1.71–1.52 Ma). The divergence time (∼22-730 ka) among H. formosensis, H. latimera, and H. tientsinensis indicates that the Taiwan Strait acted as a biogeographic barrier during major falls in sea level during the Pleistocene. Our findings indicate that H. formosensis, H. latimera, and H. tientsinensis are valid species, and that straits (Tokara Strait, Tsushima/Korea Strait, and Taiwan Strait), the Okinawa Trough, and currents (Kuroshio Current, Tsushima Current, and Taiwan Strait Warm Current) have acted as geographic barriers resulting in allopatric speciation among onshore marine animals in the northwestern Pacific.