The geographic boundaries of many important habitat-building shallow estuarine oyster (Family Ostreidae) species are poorly understood, especially in subtropical and tropical waters. These keystone species often have extensive historical and extant ranges, in part because of their ability to adapt to diverse environmental conditions and the transfer and introduction of a few species worldwide for aquaculture production. In addition, oysters exhibit morphological plasticity additionally confounding species identification and taxonomy. Molecular techniques have led to significant improvements in oyster systematics and taxonomy but have not been applied to oysters from many tropical regions, including the coastal areas of the Indian Ocean such as Bangladesh. Because species' identification based on morphological traits alone, in this case primarily shell characteristics, were inadequate, phylogenetic analyses of mitochondrial cytochrome oxidase subunit I gene fragments was also done to confirm the identity of oyster specimens collected from Bangladesh coastal waters. Phylogenetic analyses of collected oyster samples confirmed the two monophyletic subclades of the Ostreidae family Crassostrea and Saccostrea, and five oyster lineages from the region of Bangladesh were identified: Crassostrea gryphoides, Crassostrea belcheri, Saccostrea cuccullata lineage B, S. cuccullata lineage F, and Saccostrea mordax. A new addition to the list of Crassostrea species, C. belcheri was found in Bangladesh, but C. belcheri, C. gryphoides, and S. cuccullata are considered “common” species in the neighboring states of India and Myanmar indicating a widespread distribution of these species along the entire coast of the Bay of Bengal. However, S. mordax, is a new record for the Bay of Bengal region including the coastal waters of Andaman and Nicobar Islands, and thus extends the geographical distribution of this species.