Abstract: Eight types of blood proteins in serum samples from 221 Mongolian horses (including Wuzhumuqin horse, Wushen horse, Xinihe horse and Baerhu horse) were detected on polymorphism by vertical plate discontinuous polyacrylamide gel electrophoresis (PAGE). Genotype frequencies, allele frequency and genetic heterozygosity of these sites were calculated and the relationship and the genetic distance between the groups were discussed through cluster analysis.The results indicated that in addition α1-BGlycoprotein（A1B）was of monomorphism, the remaining 7 blood protein (enzyme) sites were of polymorphism in varying ways. The statistical results showed that the average heterozygosity (H) of these eight protein (enzyme) sites in Wuzhumuqin horse, Wushen horse, Xinihe horse and Baerhu horse were 0.329 6, 0.305 6, 0.378 3, 0.366 6, respectively. The cluster analysis suggested that the genetic distance between Baerhu horse and Xinihe horse was closer, however, the genetic distance between these two types of horses and the other two breeds were relatively farther.