Rodents are important host animals for many zoonoses that threaten public health worldwide.Gaining accurate taxonomic information on host animals is important for surveillance and epidemiological investigation of rodent-borne diseases.Field identification of many rodent species still remains difficult,in large part because of morphological variation through development,and color variation of pelage between individuals.Only through analysis of internal morphology (e.g.skull and dentition) can definitive identification be made.DNA barcoding can provide genetic references to validate field identifications made by researchers with limited taxonomic background,making it a particularly valuable tool for conducting ecological and epidemiological surveys.Comprehensive collection of rodent specimens has been carried out nationally and more than 90 morphologically-distinct populations were subject to DNA barcoding.Several cryptic species were found in the genera Niviventer,Rattus,and Cricetulus.The results suggested that species diversity of rodents in China is currently underestimated,especially at some hot spots of biodiversity; classification of some groups should be reviewed further; and this method will be useful in host animal identification during zoonosis surveillance.