Abstract: The present study was to develop the identification of 6 natural seeding cultivated, named FD, LJZ, FQ, PT, SSZ and XM, and 4 artificial breeding oysters population, named ND,LJR, SSR and ZA, in coastal sea of Fujian, through using multiplex species-specific PCR method. By ANOVA and Tukey multiple comparison methods, four shell morphologies from 10 breeding populations were also analyzed. A total number of 300 individual oysters were randomly collected from 10 sites along Fujian coast. Results of multiplex species-specific PCR showed that 17 samples were Crassostrea sikamea and others were Crassostrea angulata which including all artificial breeding oysters. The results indicated cultivated oysters in coastal sea of Fujian Province included Crassostrea sikamea and Crassostrea angulata, and Crassostrea angulata is dominant species. ANOVA analysis showed the values of four shell morphologies in Crassostrea angulata are greater than Crassostrea sikamea, and no significant difference was observed between the populations of FD and SSZ, SSR and XM respectively(P＞0.05), while FD and FQ, ND and LJR was significant(P<0.05).