Abstract: Oyster taxonomy has long been a matter of dispute owing to the high morphological and physiological similarities. It's an effective means to make a distinction between oysters by molecular techniques recently. We observed the morphological characteristics and measured the key measurable character indicators of the common oyster cultured in the Houhai Bay, Fujian Province. The 16S rRNA and CO I were sequenced and the phylogenetic trees involved in seven species of oysters were reconstructed based on the sequence similarities and genetic distances of 16S rRNA and CO I gene sequences in order to identify the isolated samples. Also, the electrophoretograms of isozymes (IDH, SOD) from the digestive gland tissue were analyzed. The results showed that the oyster's shell shape were different from each other because of the living environment. The oyster from the Houhai Bay should not be classified as Saccostrea cucullata but Crassostrea angulata. It was proved that sequences of 16S rRNA and CO I gene could be considered as good tools for identification in oysters. IDH and SOD were found expressing in the digestive gland tissue but no polymorphic loci was detected. The combination of morphological characteristics and molecular phylogenetic analysis has provided a good method to identify the oyster. The study lays a solid foundation for the research of the recognition and protection of germplasm resources and cultivation in C.angulata.