Abstract: Objective To understand the molecular epidemiological characteristics of rabies in Yunnan province. Methods Brain tissue samples of animals and saliva samples of patients were collected, and the presence of rabies virus was determined by direct immuno fluorescence assay (DFA) and RT-PCR. Homology and phylogenetic analyses were performed with other known sequences. Results Twenty-six of 60 samples from sick animals and 2 of 182 samples from healthy dogs were confirmed to be antigen positive for rabies virus by DFA, and the saliva samples from 4 patients and brain samples from 73 rodents were confirmed to be negative for rabies virus by DFA. Among the 28 antigen positive samples, 25 were confirmed to be nucleic acid positive for rabies virus by RT-PCR. Phylogenetie analysis indicated that DX01 and DZ01 strains in this study and some domestic rabies virus strains belonged to one branch, and DN01 strain in this study and some strains from Southeast Asia belonged to one branch. Conclusion The rabies viruses causing rabies in Yunnan were complex, which might be imported from other provinces in China and Southeast Asia.