In order to find and examine morphological differences between different ecotypes of Coilia nasus we measured the maxillary length, counted on vertebrae and anal fin ray by X-ray on 906 samples from four populations collected in Yangtze River Jingjiang in Jiangsu, Jiuduansha in Shanghai, Taihu Lake in Zhejiang, Poyang Lake in Jiangxi, respectively. The number of vertebrae and anal fin ray varied greatly no matter in the same or between different population. The number of vertebrae and anal fin ray were 81, 80, 77, 75 and 108, 109, 100, 98 in Jingjiang, Jiuduansha, Taihu Lake and Poyanghu Lake population, respectively. The ratio of maxillary length/head length in the four populations were 1.067, 1.063, 1.014 and 0.831 on average. ANOVA analysis on the number of vertebrae and ratio of maxillary length/head length indicated there was significant difference between the four populations except that between Jiuduansha and Jingjiang populations. However, the mean of anal fin rays did not showed any significant difference between all the four populations. The identification success rate between migratory population, including Jingjiang and Jiuduansha, with population of Taihu Lake and Poyanghu Lake were 92.9%, 92.8% and 99.5% by Bayes discriminant function. The results of this study indicate that C.brachygnathus and C.nasus taihuensis can be discriminated by some morphological differences although the existing research has agreed in both of them belonging to C. nasus.