Total 144 samples of Eleutheronema rhadinum species were collected from the Yellow Sea, the East China Sea and the South China Sea. Due to the widespread and ambiguous population structure of Eleutheronema rhadinum species, three multivariate analysis methods were used to comparably investigate the morphological variation of the species. By the cluster analysis, it showed the highest morphological similarity between species of Chongming and species of Qidong, also between species of Zhanjiang and Qionghai. In the principal component analysis of 32 characters of general and frame morphology, variations in the area between head and back account for the largest contribution ratio. Subsequent discrimination functions were established by means of stepwise discrimination method, with the general prediction accuracy of 87.4%. Our study revealed that variation emerged in these four geographical species.