Abstract: Pinctada margaritifer, a kind of large pearl shellfish with tropical marine characteristics in China, can produce high-quality black pearls. It is one of the important aquatic economic species that can be selected for cultivation in China's marine ranches. In this study, Haitang Bay of Hainan (HNHT), Sanya Bay of Hainan (HNSY), Chunyuan Bay of Hainan (HNCY) and Weizhou Island of Guangxi (GXWZ) geographical wild populations were selected to conduct the correlation and path analysis of their morphological traits. This study can lay a foundation for the selective breeding work of P. margaritifer, especially the host pearl oyster for pearl production process. The results indicated that the morphological trait characteristics from different populations were different. The individuals in the HNHT population were the largest, while the HNCY population were the smallest. The largest shell width index appeared in the HNHT population (0.1711± 0.003), while the smallest in the GXWZ population (0.1525± 0.003). The largest shell weight index appeared in the GXWZ population (59.05± 1.02) and the smallest in the HNSY population (50.49± 1.08). In the four geographical populations, the total shell weights showed a significant correlation with shell height and shell width. Moreover, the shell width had a direct effect on shell weight. Therefore, it is better to choose the HNHT population for the breeding work targeting shell width and shell length, and the GXWZ population for total shell weight.