Small flat oysters of the genus Ostrea were collected from China, Japan, and the United States for identification and phylogenetic analysis. Fragments of mitochondrial cytochrome oxidase subunit I and 16S rRNA genes were sequenced in 57 specimens. Shell morphology and phylogenetic analyses identified four closely related groups in the Ostrea stentina/equestris/ aupouria species complex, supporting recent and ongoing speciation. Groups 1 and 2 are both O. equestris (Say, 1834), representing two divergent populations from the Asian Pacific and the Americas, respectively. Groups 3 and 4 are two separate species independent of O. equestris. Group 4 is O. stentina occurring in northern Spain, Portugal, Morocco, and northern Tunisia. Group 3 is a new species Ostrea neostentina sp. nov. found in southeastern Spain, eastern Tunisia, Hong Kong, and Japan. The occurrence of O. equestris in both Atlantic and Pacific oceans, from Argentina, Columbia, the United States, Gulf of California, Japan, and China to New Zealand, is unusual and highlights wide connectivity of Ostrea species as part of the marine ecosystem. This study provides the first record of O. equestris and O. neostentina sp. nov. along the southern coast of China and adds to the understanding of the diversity, global distribution, and evolution of Ostrea species.