Abstract: In this research，morphological and microsatellite molecular markers are used to analyze the morphological differences and genetic diversity of four wild Paratapes undulatas populations in area of southern Fujian (SF) and Beihai Sea, Guangxi. The outcome of cluster and major constituent analysis indicates that the morphologies of Beihai and Yunxiao populations of SF are the closest，followed by Hui'an of SF. However, Xiamen population of SF has the largest divergence. Two major constituent parameters are determined，of which the contribution rate of PC1 is 36.134%，the contribution rate of PC2 is 21.443%，and the accumulated contribution rate is 57.577%. The discriminant functions of four populations were formed. The precision of P₁ is 43.3%-93.5%，P₂ is 44.8%-88.0%，and the comprehensive discriminant rate is 66.1%. The overall genetic diversities of the four clam populations are relatively high，and the genetic differentiation between populations is weak. They belong to the same free mating population. The NJ tree clustering results did not detect that the pedigree structure corresponding to the geographical locations，which may be related to the frequent gene exchange between different populations of P. undulatas caused by human introduction，trade，proliferation and other activities. It is suggested that the protection of local germplasm resources should be strengthened in the future resource management for the development and utilization of P. undulatas.