In oder to reconstruct the molecular phylogeny of Pinctada, partial sequences of 3 mtDNA fragments (12S rRNA, 16S rRNA, COⅠ) from 5 species of Pinctada (P. martensii, P. maxima, P. margaritifera, P. maculata, P. nigra) were amplified by polymerase chain reaction (PCR) and directly sequenced, and the samples were collected from Leizhou Peninsula. Base ratio and genetic distances were analyzed. At the same time, these sequences were compared with the published sequence of P. albina. Results showed that A+T contents of 3 mtDNA fragments from 5 species were higher than G+C obviously, in accordance with the other invertebrate mtDNA sequences. Data showed that the sequences of 3 mtDNA fragments had a high degree of saturation. Analysis showed that the molecular phylogenetic trees were basically constructed and well supported the traditional morphological taxonomy. In the relations of P. nigra and P. albina, 3 mtDNA fragments were very similar in nucleotide composition, genetic variability, genetic distance and molecular phylogenetic trees. So this suggests that P. nigra and P. albina represented two subspecies in the same species. About the taxonomy of P. maculata, the molecular phylogenetic trees showed that P.maculata was close to P. nigra and P. albina.Moreover, it revealed P. margaritifera and P. maxima were more primitive than the others. There was a little difference on the genetic relationship analysis about P. martensii by 3 mtDNA fragments, and no conclusion could be drawn from the existing data. It is necessary to do more study of molecular systems and morphological and anatomical structure.