To resolve the taxonomic status of a small cupped oyster from southern China, we collected and sequenced oysters from 20 sites in China along with sister species from other parts of the world. A total of 187 oysters were sequenced for 2 fragments belonging to the mitochondrial 16S rRNA and cytochrome oxidase I (COI) genes. Sequence analyses of both gene fragments indicate that the small cupped oyster from southern China is the same species as Crassostrea angulata from Portugal. C. angulata has a wide distribution in southern China, ranging from Zhejiang to Hainan, with the Yangtze River separating it from Crassostrea gigas in northern China. The wide distribution and high gene diversity in China support the suggestion of a historical transfer of C. angulata from China to Europe. Sequence divergence between C. angulata and C. gigas, 1.05–1.32% in 16S and 2.22–3.37% in COI, is higher than that between the most divergent populations of a Crassostrea species (C. virginica, 0.51% in 16S and 2.04–2.22% in COI), but considerably lower than that observed between two closely related sister species (2.11–2.37% in 16S and 9.32–10.11 % in COI, between C. gigas and Crassostrea sikamea). This finding and the fact that the two oysters live in the same region with slightly different biological characters but can hybridize without any difficulties suggest that C. angulata should be considered a subspecies of C. gigas.