Abstract: To compare the morphological differences among 9 small yellow croaker (Larimichthys polyactis) populations, we analyzed 20 morphological characteristics and 8 meristic counts of 208 individuals collected from Bohai Sea, Yellow Sea and East China Sea during 2005~2010 by using multivariate statistical analysis (principal component analysis, discriminant analysis, cluster analysis and One-Way ANOVA). The results show that the total accuracy of discrimination for the 9 populations is 73.6%, with the highest 86.4% in Ningbo and the lowest 54.3% in SY4. The results of principal component analysis, cluster analysis and One-Way ANOVA are consistent, which indicates that geographical variance exists between Bohai Sea population and other populations from Yellow Sea and East China Sea.