In order to explore the different ecotypes in the life history of tapertail anchovy between its Coilia nasus and C. brachygnathus which live in Jingjiang section of the Yangtze River, an electronic probe microanalyzer was applied to analyze the micro-chemistry patterns of element Sr and Ca in otoliths of these two fishes collected from the Jingjiang section of the Yangtze River. Analysis results on the line transect showed that the Sr/Ca ratio (i.e., Sr/Ca×10³) in the otolith of C. brachygnathus was consistently low (around 2.00), indicating that these individuals experienced in freshwater habitat during its whole life. In contrast, C. nasus had a fluctuation pattern of Sr/Ca ratio in the otolith from low to high, suggesting the individuals experienced not only in the freshwater, but also in the brackish water at different stages in their life history. All these differences could be well confirmed by the freshwater coefficient (F_C). The value of F_C in the C. brachygnathus was 1.00, and in contrast, the values of F_C in the C. nasus for the individuals collected in 2013 and 2014 were 0.36±0.06 and 0.50±0.11, respectively. It confirmed an obvious difference of life history between C. nasus and C. brachygnathus, as well as C. nasus collected between different years. The present study demonstrated that the migration patterns were significantly different between C. nasus and C. brachygnathus, as well as C. nasus collected in 2013 and 2014. The resource of C. nasus in Jingjiang section might originate from different stocks with different natal waters and life history background. The water ecotypes in Jingjiang section of the Yangtze River must be the important habitat or migration channel for both tapertail anchovy.