| In this study, utilizing microsatellite three horses populations(Kazakh horse, Yi Li horse, Hybrid horse and 149 in total)were analyzed. The genetic variation of population of 7 microsatellite locis (HMS3, HMS6, HMS7, HTG4, UM011, UCDEQ440, UCDEQ505) were analyzed by using DNA extraction, PCR amplifying, polyacrylamide gel electrophoresis testing et al. The results are showed as follow: (1) There are 41 alleles in seven microsatellites ites in these three populations, 26 alleles are found in commonin the three populations. There are 12 alleles in the locus of HMS3, which is the largest number alleles in all. There are 10 alleles in the locus of UM011. There are 9 alleles in the locus of HMS6 and HMS7. There are 8 alleles in the locus of HTG4. There aer 7aleles in the locus of UCDEQ505. And there are only 4 alleles in the locus of UCDEQ440. (2) The average heterozygosity in all populations which varied from the highest in Hybrid horse population(0.7379) to the lowest in Yi Li horses population (0.6838)respectively ; and The average PIC which varied from the highest in Hybrid horse population (0.7066) to the lowest in Yi Li horse population (0.6477)respectively. (3) The average heterozygosity and average polymorphism information content (PIC) and average numbers of alleles are 0.6838～0.7066, 0.6477～0.7066和3.5707～4.3180, respectively among these populations. (4)The genetic distances between population and the dendrogram of relationships were obtained. The genetic distances between Kazakh horse population and Hybrid horse population is nearest(0. 6121). The genetic distances between Kazakh horse population and Yi Li horses population is furthest(0.7649).
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