Genetic structure and differentiation of Reaumuria soongorica population from the desert of Fukang, Xinjiang were assessed by the means of random amplified polymorphic DNA(RAPD) markers. The results show that the higher genetic diversity and the genetic differentiation exist in the population of Reaumuria soongorica, which is composed of 7 subpopulations and 136 individuals, generated by 15 primers. 71 loci have been detected and 69 were polymorphic. The mean proportion of polymorphic loci (PPB) was 97.18%. The analysis of Shannon phenotypic diversity index (0.3075), Nei's gene diversity index (0.3127) and GST (0.3120) indicates that there were more genetic variations within the subpopulations than those among the subpopulations. The gene flow among the subpopulations of Reaumuria soongorica (Nm=1.1028, Nm>1) was much less than that of the common anemophytes (Nm=5.24), so genetic differentiation occurred to some extent. The results of AMOVA analysis show that 61.58% of the genetic variations exist among the subpopulations, and 38.02% within subpopulations. Additionally, through the use of clustering analysis, principal factor analysis and the correlation analysis, we found that the genetic structure of natural population of Reaumuria soongorica was related to some ecological factors (soil factors mainly) of the oasis-desert transition zone. The genetic diversity level of Reaumuria soongorica had the negative correlation with the content of soil total P and Cl- significantly (P<0.05), on the contrary, it had the positive correlation with CO32- significantly (P<0.05), showing that the distribution of the individuals of Reaumuria soongorica in sampling sites correlates with certain soluble salt, Furthermore, the genetic diversity of the natural population of Reaumuria soongorica increased with the decreasing of the content of organic matter, water, total N and total P in soil. This suggests that there are some relations with more potentiality of the genetic variation of Reaumuria soongorica in its long-term evolution to adapt worse environment.