Shell morphology of oysters is plastic and sensitive to environmental influence. It cannot be used as reliable characters for species identification. This has led to many errors and confusions in oyster classification.DNA barcoding promises a useful tool for species identification, and also to elucidate the phylogeny of oysters. In this preliminary study we examined 140 OTUs for phylogenetic analysis. To investigate the possibility that concordance between species based on COI barcodes and compare with traditional morphological view. The result of this study showed that 2 genera (Crassostrea and Saccostrea) were found. Pure population of C. angulata was observed in Taiwan. Six groups of unidentified oysters (Crassostrea sp. and Saccostrea sp. groups 1, 2, 3, 4, and 5) were also genetically analyzed.