Barbless Carp (Cyprinus pellegrini), which is endemic to lakes of Yunnan plateau, is categorized into the second grade in the list of China key protected animal species. Introgressive hybridization between native Barbless Carp and exotic Common Carp (C.carpio) has occurred extensively in Xingyun Lake. This study assessed the genetic status of the Luosipu original population of Barbless Carp based on morphological, microsatellite and mitochondrial DNA analyses. Morphological analyses showed that all individuals of the Luosipu Barbless Carp sample were strictly intermediate between reference samples of Barbless and Common Carp. Factorial correspondence analysis of microsatellite data indicated that all individuals of the Luosipu Barbless Carp sample fell in between reference samples of Barbless and Common Carp, but were very near to the former. Mitochondrial DNA analysis revealed that all individuals of the Luosipu Barbless Carp sample had the mitochondrial DNA haplotypes of Common Carp. There was obvious inconsistency between nuclear and mitochondrial genetic structures in Luosipu Barbless Carp sample. These results suggest that all individuals of the Luosipu Barbless Carp sample are hybrids. Considering that the Luosipu Barbless Carp population may in fact be a hybrid population, a new captive breeding programme should be found for effectively conserving and restoring Barbless Carp.