Although morphology has been successfully used to distinguish wild Chinese mitten crabs (Eriocheir sinensis) from the Yangtze River and the Minjiang River, whether morphology could be used to identify the pond-reared offspring of these two wild E. sinensis populations still remains unclear. This study was undertaken to examine the morphological difference of wild E. sinensis (G0) from the Yangtze River (YZ) and Minjiang River (MJ) as well as their pond-reared offspring (G1). The results showed that:G0 populations were clearly divided into two independent groups by the first two principal components in the principal component analysis, but the plots were completely overlapped between two G1 populations; the grid distortion map showed that morphological differences of various populations are mainly manifested in the frontal and lateral spines of carapace; the discriminative accuracies of two G0 populations in the stepwise discriminant analysis both are 100%, but the discriminative accuracies of two G1 populations were 40%-60% with obvious misjudgment risk; cluster analysis showed that two G1 populations were clustered firstly and then were clustered with G0 of YZ population, while G0 of MJ population was formed into another distinct cluster. In summary, morphological differences between two wild E. sinensis populations disappeared after one generation of artificial culture, and morphology thus probably cannot be used to distinguish the pond-reared offspring of wild E. sinensis populations originated from the Yangtze River and Minjiang River.