AbstractBackgroundRhizosphere microbes possess important effects on plant growth and quality. Here we collected tobacco roots and leaf samples from ten places in Yunnan province to investigate the interaction of the rhizosphere microbes, the soil physicochemical characteristics, and the tobacco leaf properties. ResultsA high-throughput sequencing method was used to sequence the V3–V4 region of 16S rRNA genes, and the operational taxonomic units (OTUs) were clustered using QIIME under 97% identity. A total of 4571 OTUs were obtained from the 30 tobacco root samples, and the top three phyla were Proteobacteria, Acidobacteria, and Actinobacteria, while the top three annotated genera were Gp6, Gemmatimonas, and Gp4. Redundancy analysis (RDA) showed that most of the soil physicochemical properties (10 out of 17) had a significant influence on the rhizosphere microbial community. Both correlation analysis and RDA analysis revealed that quick potassium (K) and Acidobacteria_Gp3 had a significant correlation with the tobacco leaf properties. The variance partitioning analysis showed that rhizosphere microbes had a bigger influence on the tobacco leaf properties. ConclusionsOur results showed great differences in the rhizosphere microbial diversity of tobacco and complex interaction among the microbial diversity, soil physicochemical characteristics, and tobacco leaf properties.