We used noncoding chloroplst DNA sequence (trnLtrnF and trnDtrnT) to study the genetic diversity of 16 populations of Salix psammophila distributed in Mu Us Sandy land and Kubuqi deserts,which aimed to explore genetic diversity, structure and differentiation characteristics of this species. This study provide theoretical basis for genetic management, improvement, breeding and variety selection of S. psammophila. The main results showed that： (1) the length of combine sequences was 1 811 bp, a total of 12 nucleotide mutation sites were identified and 16 haplotypes were recovered, including 8 simple information sites and 4 mutation sites. (2) The haplotype diversity was 0.737. The nucleotide diversity was 0.001 07. Only haplotype H3 located in the center of the haplotype network map distributed in all populations, while other haplotypes were randomly distributed among the populations. (3) AMOVA analysis suggest that 91.16% of the total variation existed within population while among population variation was medium (F_ST = 0.088 37). The exchanging of gene between the populations was very frequent (N_m=2.58). There is significant phylogeographic structure in population of S. psammophila. (N_ST=0.085, G_ST=0.056, 0.01 < P < 0.05). (4) Neutral tests and mismatch analysis proved that the distribution of S. psammophila population did not expand significantly.