One hundred and fifty seven individuals of Japanese Spanish mackerel Scomberomorus niphonius were collected from five geographic populations in the northern Yellow Sea (Dongying and Weihai) and East China Sea (Zhoushan, Ningbo and Wenzhou), and 20 individuals of IndoPacific king mackerel (S. guttatus) were also collected from Guangzhou, Guangdong Province, as outgroup. One way ANOVA analysis, principal component analysis and cluster analysis were applied in this study. The result of one way ANOVA revealed significant difference (P<0.05) in means of SP/FL, VA/FL, pectoral fin rays and gill rakes between the Yellow Sea and East China Sea populations, and there are significant differences between two species in most of morphological characteristics. According to Mayr 75% rule, the differences among the five populations were still below the population level. By principal components analysis, three principal components were established, with their contributory ratios being 32.32%, 11.92% and 7.67%，respectively, and the cumulative contributory ratio was 51.91%. The plot of first and second component showed that there were significant differences between the Yellow Sea and East China Sea. The results of cluster analysis revealed that the two populations from the Yellow Sea were pooled into one group, while the other three populations from the East China Sea were pooled into another group, and the significant geographical variances were detected in this species.