Although oysters are important aquaculture and fishery species as well as keystone species in coastal and estuarine ecology, their global species diversity is not fully understood due to problems of oyster classification. Molecular taxonomy has contributed to oyster classification but not been applied to oysters from many regions including Myanmar. In this study, oysters from Myanmar were collected and subjected to taxonomic analysis with mitochondrial cytochrome oxidase I and 16S rRNA sequences. Sequence analysis reveals that the Myanmar oysters collected in this study belong to three species: Saccostrea malabonensis (Faustino, 1932), a distinct member of the superspecies Saccostrea cucullata (Born, 1778) group; Crassostrea belcheri (Sowerby, 1871), a common species found in Indo-Pacific; and Crassostrea gryphoides tanintharyiensis, a sister subspecies of Crassostrea gryphoides dwarkaensis from Arabian Sea that is different from the fossil species Crassostrea gryphoides (von Schlotheim, 1813). Results of this study highlight the need for molecular taxonomy of oysters from all world oceans to understand and protect the species diversity of this important species group.