Abstract: Estuarine tapertail anchovy Coilia nasus is believed as a “flagship species” “indicator species” and “umbrella species” for protection of the Changjiang River ecological system. In order to reveal the otolith morphological characteristics and population delineation/identification of C. nasus in Anhui section of the Changjiang River, the landmark-based geometric morphometric analysis was utilized to comparatively study the sagittal otoliths of two ecomorphotypes (i.e., the long supermaxilla C. nasus and short supermaxilla C. brachygnathus) and five populations of the anchovy in Anqing and Tongling sections of the Changjiang River in Anhui Province. The left sagittal otolith of each specimen was used in the present study. A Leica M205A stereo microscope was used to photograph the otolith samples. Subsequently, tpsDig2 software was used to establish and measure the landmark points on the otolith photos. Based on 12 landmarks, the coordinates were analyzed by relative distortion component analysis and discriminant analysis. The morphological variation vectors were then visualized through thin plate spline analysis and mesh deformation. The results show that most of the extracted landmarks are type Ⅱ landmarks, and their contribution rate is 69.48% in the analysis of relative distorted main components, indicating that type Ⅱ landmarks were the main source of otolith morphological differences. The general discriminant accuracy of the five populations was 95.6%, indicating that significant differences in otolith morphology were generally existed among the populations of C. nasus. Especially, 100% classification accuracies were achieved for the variation between long supermaxilla C. nasus and short supermaxilla C. brachygnathus, as well as among 3 populations of long supermaxilla C. nasus. Therefore, it will be reasonable to believe that the differences of otolith morphometrics particularly observed in the long vs. short supermaxilla ecomorphotypes and 3 populations of long supermaxilla C. nasus could reflect the evidences of ecomorphotype differentiation and high/low level population connectivity. The aforementioned findings can provide theoretic basis and supports for objective evaluations of resource composition and population difference of C. nasus in Anhui section of the Changjiang River before and after the 10-year fishing ban policy. Furthermore, this study provides an important reference case for population delineation or identification of different ecomorphotype C. nasus in other waters and other commercial fish resources the Changjiang River Basin.