Bacteria are the most abundant soil microbes and are sensitive to environmental change, especially soil carbon (C) and nitrogen (N) dynamics. The bacterial diversity of rhizosphere and bulk soils associated with desert plants is not well understood. In this study, we measured the properties of rhizosphere and bulk soils at different depths (0-20, 20-40, 40-60, and 60-80 cm), the diversity of bacterial communities (16S rDNA amplicon sequencing), and their relationships with Anabasis aphylla in the southern margin of the Gurbantunggut Desert, Junggar Basin, China. A total of 11,420 operational taxonomic units (OTUs) were obtained from 40 soil samples, belonging to 641 genera, 269 families, 137 orders, 61 classes, and 44 phyla. There were significant differences in electrical conductivity (EC), available nitrogen (AN), available phosphorus (AP), available potassium (AK), and bacterial diversity. The dominant bacterial communities of the rhizosphere and bulk soils at the phylum level were Actinobacteria, Proteobacteria, and Bacteroidetes. At the genus level, the dominant communities of the rhizosphere and bulk soils were Halomonas and Glycomyces, respectively. At different soil depths, the abundances of bacteria in the soil were 10.2% (0-20 cm) > 8.4% (20-40 cm) > 8.3% (60-80 cm) > 6.2% (40-60 cm). Our results indicate that bacteria in the phyla Actinobacteria and Proteobacteria, as well as the genus Halomonas, are key to the drought and salt tolerance of A. aphylla.