Abstract: To clarify the response of bacterial communities of cigar tobacco infected with the pathogen of black shank and to explore their biocontrol potential in green disease prevention and control, high-throughput sequencing technology was used to analyze the community compositions and structures of bacteria in rhizosphere soil, bulk soil and stalks of healthy and infected cigar tobacco. The results showed that pathogen infection significantly altered the community composition and structure of bacteria in rhizosphere soil, bulk soil and stalks of cigar tobacco. The structures of endophytic bacterial community in the infected area and at the junction between infected and healthy areas of stalks were significantly different with that in healthy stalks at various taxonomic levels. The bacterial communities in rhizosphere soil and bulk soil of both healthy and infected cigar tobacco plants were mainly composed of Proteobacteria and Actinobacteria at phylum level, while in tobacco stalks were Proteobacteria and Firmicutes. In the stalks of healthy tobacco plants, the dominant bacterial genera were Pantoea, Pseudomonas and Massilia, while in the stalks of infected tobacco plants were Ralstonia and Sphingobacterium. Additionally, in the junction of infected and healthy stalk, the relative abundances of Bacillus and Bacillus aerophilus were significantly higher than those in the infected stalks. PICRUSt gene function prediction revealed that the relative abundance of functional genes related to environmental information processing of bacterial community in healthy tobacco plants was significantly higher than that in the infected tobacco plants. Overall, significant differences existed between healthy and infected tobacco plants in terms of bacterial community structure, diversity, dominant bacterial genera and gene functional pathways, and the bacterial community in the stalks was more sensitive to pathogen infection than that in rhizosphere soil.