Eleven pairs of simple sequence primers were used to analyze genetic diversity and genetic structure of wild Prunus tomentosa Thunb.including 104 ecotypes,11 subpopulations and 5 populations from Qinling Mountain,in order to make clear of cherry germplasm resources in China,and provide theoretic reference for cherry breeding and cherry root stock modifying.The results showed that:(1)A total of 110 alleles of 11 loci were detected from 104 individuals and 5~13 alleles could be detected from each primer.The observed average number of alleles (A) was 10;the effective number of alleles (Ae) was 7.586 3.(2)The percentage of polymorphic loci (PPB) was 69.55% in Tianshui Valley,76.53% in Chang’an Valley,81.36% in Taibai Valley,85.00% in Huayin Valley,92.17% in Meixian Valley,and the total PPB was 81.62%.The higher level of expected heterozygosity (He) was 0.864 0.(3)The coefficient of gene differentiation (Gst) was 0.081 2,about 91.88% of gene differentiation was observed within the population,and 8.12% among the populations.Gene flow (Nm) was 2.827 3.The total Nei’s genetic distance was 0.489 7 and Shannon’s information index was 2.101 9.The research indicated that higher level of genetic diversity existed in wild P.tomentosa Thub.in Qinling Mountain.The genetic differentiation within population was higher than that among populations,and gene exchange was not hindered.It was not sensitive to genetic drift in the existing level of genetic diversity within population.However,moderate gene exchange existed among populations may reduce the redifferentiation of entire populations.