Abstract: To explore the characteristics of soil microbial communities of Cistanche deserticola and Cynomorium songaricum, two typical parasitic medicinal plants that live in an extreme saline alkali environment, 16S PCR was used to sequence the soil microbial communities of C. deserticola and C. songaricum in Ebinur Lake, Xinjiang. Redundancy analysis and correlation analysis were carried out based on the abundance of core microbiome and ecoclimatic factors. The results show that the diversity of the soil microbial community of C. deserticola was significantly higher than that of C. songaricum. The core microbial groups of C. deserticola and C. songaricum were Marinomona, Halomonadaceae, Rhizobiales, Halomonas, and Acidimicrobiales. Six specific biomarkers were identified as Micrococcacea, Echinicola, Glutamicibacter, Galbibacter, Pseudoalteromonas, and Marinobacterium_rhizophilum. The results of redundancy analysis and correlation analysis show that the average temperature in the driest season and the average temperature in the coldest season, and the clay content and soil texture classification were the main ecological factors affecting the composition of these soil microbial communities. This study provides a theoretical basis for finding molecular markers of C. deserticola and C. songaricum and promoting the quality of C. deserticola and C. songaricum.