Abstract: One-way Analysis of Variance （ANOVA）， cluster analysis， principal component analysis and multivariate discrimination analysis were used to study the morphological variations of wild populations of Manila clam Ruditapes philippinarum from 5 sea areas of Nanpu， Haizhou， Laizhou， Putian and Shanwei. One-way ANOVA showed that the clams of Haizhou group were significantly different from those of other groups in many morphological parameters. Cluster analysis indicated that the populations of Nanpu， Laizhou， Putian and Shanwei were morphologically similar except for Haizhou population. Principal component analysis showed that 2 principal components had contributory ratios of 28.28% and 20.77%， respectively， with a cumulative contributory ratio 49.05%. The scattering diagram showed that Haizhou group differed remarkably from other groups. The discriminant functions of 5 groups were established. As results the discriminant accuracy rate was 36.0%-80.0% （P1，P2）， with a total of 53.6%， among which the discriminant accuracy rate of Haizhou group was the highest. To summarize， Haizhou group was morphologically significant different from the other four groups. This study can be helpful for germplasm resources protection and hybrid breeding of Ruditapes philippinarum．