Hybridization with introduced fish species is an important threat to native fish species. Here we investigated hybridization between native barbless carp (Cyprinus pellegrini) and introduced common carp (C. carpio) in Xingyun Lake in the Yunnan-Guizhou plateau of China. A total of 203 individuals of Cyprinus from Xingyun Lake were studied by combination of morphological and genetic analyses. Most individuals were strictly intermediate between the two parental species in morphology, strongly suggesting that extensive hybridization has occurred. Bayesian model-based clustering of the genetic data suggests that there are two distinct genetic groups corresponding to barbless and common carp respectively. Many individuals in the two genetic groups showed intermediate morphology, suggesting that both groups actually contain massively introgressed genes. Only two individuals were identified as barbless carp both morphologically and genetically, hinting that this native species is at risk of genetic extinction in Xingyun Lake.