Abstract: In order to study morphometry differences in Chelon affinis populations, both variations of morphological character and otolith morphometry were compared by multivariate statistical analysis based on the samples collected from six populations in the coastal waters of Jinmen, Xiamen, Humen, Zhanjiang, Beihai and Fangchenggang.The morphology study was carried out used both traditional morphology and landmark morphology and otolith morphology was studied by the combination of traditional otolith morphology analysis and elliptic Fourier analysis. Similar results were obtained by the study of morphology and otolith morphology.The results of principal component analysis showed that the first 8 principal components extracted from 28 morphological characters explained 65.868% of the total variance and that 79.290% of the total variance could be explained by the first 23 principal components extracted from 85 otolith morphological indices. Therefore, it could be concluded that the difference of morphology and otolith morphology among C. affinis populations could not be presented by only a few indices according to the critical value(85.000%). The correlations among geographic distribution and morphological and otolith morphological variations were presented in cluster analysis. The results of the discriminant analysis showed that the average classification ratio based on morphological characters was 75.9% compared with lower value 69.3% based on otolith indices. It was found that with oneway ANOVA analysis on the morphological measurements the Zhanjiang population had the least indices different significantly from the other populations. On the one hand, the differences in diet composition, habitats and currents may lead to the existent variations of morphology and otolith morphology. On the other hand, the similarity of physicochemical factors and communications among groups would reduce their differences.