Abstract: The ITS 2 complete sequences and flanked 5.8S and 28S rDNA partial sequences of six pearl oysters, namely, Pinctada maxima, P.margaritifera, P.albina, P.nigra, P.chemnitzi and P.fucata in the genus Pinctada were analyzed, among which the sequences of P. nigra were obtained from GenBank. The PCR product is about 600 bp, which contains 84 bp of 5.8S and 272 bp of 28S rDNA fragments(both including primer sequence). The full length of ITS 2 ranges from 211 to 254 bp. The sequence variation analysis indicated that 5.8S and 28S rDNA fragments are highly conservative and not suitable for species identification whereas ITS 2 is highly variable with 146 mutation sites (including 72 insertion/deletions) within 270 alignment positions. The interspecific genetic distances are much greater than the intraspecific distances except that between P.albina and P. nigra. The genotype analysis also demonstrated that each species has its own genotypes. These findings suggested that ITS 2 is a high-resolution molecular marker useful in identification of species, hybrids, larvae and tissue samples of the pearl oysters.