Abstract: Landmark-based morphometric analysis was first used to identify the variation in the otolith and stock connectivity of Coilia mystus and C. grayii from the Pearl River estuary and Jiulong River estuary. Six landmarks in the outline of otolith and four landmarks in the sulcus were selected to extract the geometric morphometric information of otoliths. Discrimination analysis indicates that both intra-and inter-species distinguishing ratios of the two Coilia fish from two different waters were 100%. Among the 10 landmarks, those in the sulcus had main contribution (76.1%) in explaining the main source of morphological variation, while those in the outline of otolith just had 23.9%. The difference of inter-species shows that the sulcus of C. mystus was wider than C. grayii. Meanwhile, the difference of intra species shows that the C. grayii from the Pearl River estuary, had a narrower sulcus than those from the Jiulong River estuary, but the two stocks of C. mystus from these two waters were the opposite. It is revealed that the investigated stocks of either C. mystus or C. grayii from the Pearl River estuary and Jiulong River estuary are separated, which means that they may belong to different geographical stocks.