Abstract: 【Objective】 To explore the structural richness and diversity of endophytic microbial communities associated with rhizosphere soil and leaves in the saline-alkali environment of Xinjiang. 【Methods】 The 16SrDNA-V4 region amplicon and ITS1 region were sequenced in rhizosphere soil and leaves of Nitraria through Novaseq sequencing system.After each sample was amplified and fused by FLASH, and chloroplast genome sequence and mitochondrial sequence were filtered by Qiim, sequences were finally obtained respectively.With 97% sequence similarity, these sequences were clustered into Operational Taxonomic Units (OTUs).Bioinformatics analysis was carried out on the sequence data to evaluate the species Chao1 index, Shannon index and Alpha diversity. 【Results】 The results showed that the dominant bacterial microflora of Nitraria in rhizosphere soil were Actinobacteria, Proteobacteria, Gemmatimonadetes; And the dominant microflora of fungi was Ascomycota, the dominant endophytic bacterial microfloras were Cyanobacteria and Actinobacteria; and the dominant microflora of fungi was Ascomycota.There were significant differences in the number and diversity of microflora in different parts of Nitraria (P<0.05).There were obvious differences in the composition of microbial communities among various species. 【Conclusion】 The richness and diversity distribution of microbial community in different parts of Nitraria are revealed by high-throughput sequencing technology, which has provided theoretical basis for the selection of PGPR strains, the improvement of saline soil and the development of microbial fertilizers.