Abstract: MiSeq Illumina sequencing platform, variance analysis, and stepwise regression analysis were used to study the microbial characteristics and their relationships with physicochemical properties of soils in central Henan tobacco growing areas. The results showed that:1) The diversity of bacteria was higher than that of fungi in soils of central Henan tobacco growing areas. The dominate bacterial phylum were Acidobacteria, Proteobacteria, Actinobacteria and Planctomycetes, and the dominate fungal phylum were Ascomycota, Basidiomycota and Zygomycota. 2) The bacterial content, Chao index and Shannon index of tobacco growing soils in Jiaxian and Xiangxian were extremely significantly higher than those in Biyang, however there was no significant difference of soil fungal diversity among the three counties. The percentage of Acidobacteria in Biyang and Jiaxian were significantly higher than that in Xiangxian. The percentage of Actinobacteria in Jiaxian and Xiangxian were significantly lower, while that of Planctomycetes in Jiaxian and Xiangxian were significantly higher than those in Biyang. The percentage of Ascomycota in Xiangxian was significantly higher than that in Biyang and Jiaxian. 3) The content of bacteria extremely significantly positively correlated to soil organic matter and pH. Chao index of bacteria extremely significantly positively correlated to pH, extremely significantly negatively correlated to alkaline nitrogen and significantly negatively correlated to available phosphorus. Shannon index of bacteria extremely significantly positively correlated to pH and extremely significantly negatively correlated to alkaline nitrogen and significantly negatively correlated to the content of water-stable aggregates. The content of fungi significantly negatively correlated to pH and extremely significantly positively correlated to available phosphorus. Shannon index of fungi extremely significantly negatively correlated to soil surface hardness, while there was no significant correlation between Chao index of fungi and soil physicochemical properties. The regression equations for the contents, Chao index and Shannon index of bacteria and fungi with soil physicochemical properties reached extremely significant level, and the regression coefficient probability of all independent variables reached extremely significant level (P < 0.01). Therefore, microbial characteristics were closely related to physicochemical properties of soils in central Henan tobacco growing areas and were mainly influenced by pH, soil organic matter, available phosphorus and soil surface hardness.