Tamarix ramosissima is one of the most widely distributed Tamarix species in extremely arid areas. It can inhabit sandy wasteland, arid salinealkali land, and salinealkali wetland, etc., and it plays an important role in maintaining the stability of a specific ecosystem and protecting the diversity of plant germplasm resources. In this study, by using 14 ESTSSR markers, we analyzed the genetic diversity and genetic structure of 12 natural T. ramosissima populations (191 individuals) in the Ejina wetlands of the Alxa area. It provides a theoretical basis for the management, protection, and utilization of Tamarix germplasm resources in the region. The results showed that: (1) a total of 79 alleles (N_a) were amplified from 14 ESTSSR markers. The average number of alleles per locus was 5.6, the average expected heterozygosity (H_e) was 0.55, the average observed heterozygosity (H_o) was 0.29, and the average polymorphism information content (PIC) was 0.51, indicating that the investigated populations had abundant information of genetic variation. (2) the average polymorphic loci ratio, the average Shannons information index (I), and the average fixed index (F) of the 12 T. ramosissima populations were 97.0%, 0.862, and 0.332, respectively, which indicated that the T. ramosissima populations in this area processed a high level of genetic diversity. (3) The mean inbreeding coefficient (F_is) within the populations was 0.366, and the average genetic differentiation coefficient (F_st) and gene flow (N_m) between the populations were 0.079 and 4.425, respectively. These results suggested that the genetic exchange between the populations existed widely, and the genetic variation within the investigated populations was significantly higher than that between populations. (4) The genetic structure analysis showed that the 12 T. ramosissima populations could be divided into four subpopulations, and the genetic distances between these populations were uncorrelated with their geographical distances (r=0.194, P=0.120). The present study identified that the investigated T. ramosissima populations had rich genetic diversity, while they all showed a certain degree of heterozygote deficiency and inbreeding, which had a potentially adverse effect on the longterm maintenance of genetic diversity of T. ramosissima in this area.