Genetic diversity was studied by RAPD analysis in 7 subpopulations and 136 individuals of Reaumuria soongorica in the oasis-desert transitional zone of Fukang, Xinjiang, China. The experiment involved the different microenvironment stresses (ecological factors) in the oasis-desert zone of Fukang: (1) geographical location, including latitude and longitude; (2) the components of the soil, such as the content organic matter, N, P, K, water, salinity and pH value. Comparisons were based on 71 loci amplified by 15 oligonucleotide primers. These DNA polymorphisms appeared to be associated with the microenvironment stresses. The results indicated that the significant correlation existed among the ecological factors in the different microenvironments. And the allele frequencies of 39 from 71 loci highly related with the corresponding microenvironment factors. The mean proportion of polymorphic loci (P), Shannon information index (I), Nei’s gene diversity (H), observed number of alleles (Na) and effective number of alleles (Ne) of R. soongorica seven subpopulations related each other to some extent. The paper showed that the microenvironment stresses (ecological factors) played the important role in adaptive genetic differentiation of R. soongorica population, which resulted from the natural selection, and not by chance from subpopulation subdivisions.