Abstract: In this paper,using protein electrophorsis,we analyzed two different populations of Yunnan horses,the Yunnan common horses (21 individuals) and the short horses(14 individuals).Of all the 44 genetic loci surveyed,10 of them were found to be polymorphic.Therefore,as for the common horse population,the percentage of polymorphic loci(P) is 0.227,the mean heterozygosity(H) is 0.089 and the mean number of allels(A) is 1.273.In short horse population,P=0.205,H=0.083,A=1.250.The above results indicated that both the common and short horse populations were wealthy of genetic diversity.There existed many variations of alleles in the two populations from limited areas of Yunnan Province.Futhermore,we calculated Neis genetic distance (D) between the two populations and got a value of 0.0317,which imply a certain degree of genetic differentiation between them.According to the hypothesis of molecular clock,we speculated that the divergent event occurred about 18.5 million years ago.