In this study，in order to explore the relationship between the different incidence of tobacco black shank and soil ecological environment factors，to clarify the factors related to the incidence of black shank，and to provide a theoretical basis for the future biological epidemic prevention of black shank，the rhizosphere soils (disease grades:0，5，7，and 9) with different incidences of tobacco black shank were collected through field investigations，and the soil physical and chemical indexes and enzyme activities were determined，and 16S DNA and ITS gene sequencing technologies were used. The differences of bacterial and fungal community structure in the rhizosphere soil of diseased and uninfected tobacco plants were analyzed. The results showed:(1) Alkali-hydrolyzable nitrogen (AN)，nitrate nitrogen (NO^3--N)，ammonium nitrogen (NH4+-N)，available phosphorus (AP)，available potassium (AK)，sucrose enzyme (SUC)，catalase (CAT) and acid phosphatase (ACP) increased by 197.53 mg/kg，82.67 mg/kg，33.17 mg/kg，65.7 mg/kg，358.07 mg/kg，8.84 mg/(d·g)，56.80μmol/(h·g)，3938.69 nmol/(h·g)， respectively，compared with normal soil and there were significant differences among the treatments (P<0.05)；(2) Compared with the uninfected soil，the diversity of bacterial and fungal community structure of the diseased soil was low，and the diversity gradually decreased with the increase of the disease degree；(3) The relative abundances of B.Firmicutes，F.Nicotiana，F.Fusarium，F.Setophoma in the diseased soil were higher than those in the normal soil，while B.Proteobacteria，B.Actinobacteria，B.Acidobacteria，B.Chloroflexi，B. Planctomycetes，F.Mortierella，F.Gongronella and F.Saitozyma community abundances were lower than those in the normal soil；(4) The indicator species analysis showed that compared with normal soil，B.Actinobacteria，B. Acidobacteria，B.Firmicutes，F.Gongronella and F.Setophoma had significant positive responses and were the indicator species for disease occurrence；(5) Redundancy analysis (RDA) showed that B.Actinobacteria，B.Acidobacteria and F.Gongronella were associated with disease occurrence and were negatively correlated，whereas B.Firmicutes and F.Setophoma were the opposite. In conclusion，the increased relative abundances of B.Actinobacteria，B.Acidobacteria，and F.Gongronella and the decreased relative abundances of B.Firmicutes and F.Setophoma in the rhizosphere soil were important microbial factors for the pathogenesis of tobacco black shank.