Abstract: In this paper,using protein electrophoresis,we analyzed three species of Apodemus derived from Yunnan Province,A.chevrieri,(8 individuals) A.draco (3 individuals) and A.latronum (1 individual),and 3 individuals of Hapalomys delacouri as outgroup.Products of 27 genetic loci were surveyed,21 of them were found to be polymorphic.We input the data of gene frequences into the PHYLIP program called"Continuous character maximum Likelihood method version 3.5",and got an unrooted tree displaying the genetic relationship among the above species.The unrooted tree indicated that H.delacouri is obviously different from the others consisting a separate group outside,and A.draco also consisted a group repectively while A.latronum was in the A.draco group.According to our results about protein electrophoresis and other studies from morphology and mitochondrial DNA RFLP,we suggested that the A.latronum is closely realated to A.draco while A.chevrieri are genetically different from them to a certain degree.All the three species can be recognized separate species.