This study was carried out to compare the fish body indicators, content and activity of digestive enzyme, basic nutrition and fatty acids components in the muscle of juvenile Coilia nasus and Coilia nasus taihuensis samples which were collected from the Yangtze River and Taihu lake, respectively. The nutrition value of the two species of Coilia and the effects of different ecological habitats were also evaluated. The results showed that:（1）The activity of digestive enzyme of C. nasuswas lower than that of C. nasus taihuensis , however , the difference was on the lipase activity of C. nasus which was 3 times higher than C. nasus taihuensis. Lipid peroxides which is harmful substances was not accumulated to large amount in C. nasus. (2) Crude fat content in C. nasus was 16.13%, which was 1.5 times higher than C. nasus taihuensis while crude protein was lower in C. nasus taihuensis. (3) There were 21 kinds of fatty acid components in juvenile C. nasus while only 17 in C. nasus taihuensis. The C22∶1, C24∶1, C20∶3n-6 and C20∶4n-6 fatty acids in the C. nasus taihuensis were not detected. Contents of ∑n-3, ∑n-6 and ∑n-6/∑n-3 in muscle of C. nasus taihuensis was higher than that of C.nasus, but content of EPA and DHA were significantly lower than those of C.nasus.