To determine the genetic diversity of Haloxylon ammodendron collected from 14 sites in 5 provinces, 103 H. ammodendron samples of 12 wild populations and 2 cultivated which collected from 14 sites in 5 provinces were analyzed by amplified fragment length polymorphism (AFLP) DNA markers. PopGen32 and NTSYSpc2.1 was applied to evaluate genetic diversity of H. ammodendron populations. The average percentage of polymorphic loci (PPL) of total H. ammodendron populations was 94.13%, the average Nei's gene diversity index (H(e)) from 14 populations was 0.308 0, and the Shannon's genetic diversity index (I) was 0.467 6. The results indicated that the genetic diversity of H. ammodendron populations was high. Genetic differentiation index (G(st)) was 0.313 8, and the gene flow (N(m)) was 1.093 5 at the population level. The level of gene flow of H. ammodendron showed it possessed the feature of wind-pollinated outcrossing plants. AMOVA analysis indicated that genetic variation of H. ammodendron was much higher within groups (89.34%) than that among groups (10.66%), moreover genetic variation within groups mainly occurred among populations in different producing areas (84.80%). Cluster analysis (UPGMA) was applied to generate dendrogram based on Nei's genetic distances of 14 populations. Samples from Xinjiang and Qinghai were clustered respectively as a clade for their distant genetic relationship, while Samples from Gansu, Inner Mongolia and Ningxia were clustered together for their close genetic relationship. Genetic diversity of H. ammodendron populations is high in China, and genetic differentiation among regions is small, thus abundance within this specie is high at this stage. Therefore, wild nursery and artificial cultivating in different areas are effective measures for the conservation and sustainable utilization of H. ammodendron resources.