Abstract: In the study,we used 12 wild apples groups of Xinjiang which undered the four populations of Xinjiang Gongliu,Xinyuan,Huocheng,Tuoli as materials,involving in group microsatellite allele and genotype differences analysis of 12 linkage groups with 17 pairs of SSR primers,exploring genetic diversity and genetic structure of natural populations of Xinjiang wild apples from geographic populations,the altitude and the type of primer perspective.The results showed that the percentage of intraspecific polymorphic loci in Xinjiang wild apples with 17 pairs of SSR primers was up to 100%;the genetic diversity of group XY1 and HC2 were higher.Clustering results showed that the groups undered the same population were divided in the same group;The genetic relationships of the Gongliu population and the Xinyuan population were nearest,the Huocheng population was followed,the Tuoli population was the farthest.The Huocheng population was the highest,The Tuoli population was the lowest on genetic diversity in the different regions.The impact on the population genetic structure of altitude was smaller,excepting the observed heterozygosity and altitude exist weak positive correlation,most genetic parameters had no correlation with altitude.The variation within Xinjiang wild apples populations was greater than among populations,the differentiation among populations was small,the gene flow was higher.