Abstract: To explore carapace difference between Yangcheng Lake originated Eriocheir sinensis and one-month “bathed” E. sinensis crabs, landmark-based geometric morphometric analysis was used to comparatively study the carapace characteristics of the two type crabs in Yangcheng Lake. The carapace morphology was characterized by a 35-landmark point system. After image and the punctuation coordinates were processed, relative distortion and discriminant analysis were performed. Later, the morphological variation vector was visualized by using spline analysis and mesh deformation. The stepwise discriminant analysis of relative distortion scores showed that the discrimination accuracies for both Yangcheng Lake originated and “bathed” E. sinensis crabs were 100% at before and after bathing. According to the grid deformation diagram, there was no significant change in the carapace morphology of Yangcheng Lake originated crabs during one month period, unlike the situation of the “bathed” crabs. This study reveals for the first time the carapace difference between natively originated and one-month bathed E. sinensis crabs in Yangcheng Lake, which has a strong application potential for effectively distinguishing the latter from the former E. sinensis.