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. Furthermore, the classification and the distributions of oysters in outlying islands of Taiwan are poorly understood. DNA barcodes promises a useful tool for species identification, and also elucidate the phylogeny of oysters. In this preliminary study we used DNA barcodes to investigate the taxonomic diversity of oysters of outlying islands of Taiwan and also establish the DNA database of oysters imported from foreign country. We examined 150 OTUs for phylogenetic analysis, molecular data suggest that Taiwan oyster is a diverse taxon. The result of this study showed that 3 genera：Crassostrea, Saccostrea, and Ostrea. 5 species (C. angulata, C. sikamea, S. cuccullata, S. mordax, and S. kegaki）were identified by the molecular data. On the other hand, 13 species of imported oysters were collected in market, and which were represented from 8 countries. The oysters imported from USA referred to as C. sikamea and C. gigas. The Oysters imported from Veitnam referred to as C. cuttackensis. However, the other 11 species were all referred to as C. gigas. This result showed that C. gigas is an important cultivate species in many regions of the world.