Abstract: To understand the diversity of endophytic bacteria in flue-cured tobacco, using Jiyan 9 of flue-cured tobacco as the test material, 24, 18 and 16 strains of endophytic bacteria were isolated from roots, stems and leaves of flue-cured tobacco from Wangqing, Helong and Yanji regions respectively. Preliminary identification and diversity analysis of isolated endophytes were carried out based on colony phenotypic characteristics and 16S rRNA sequence homology analysis. The results showed that the endophytes were mainly Proteobacteria, Actinobacteria, and Firmicutes. Among them, Bacillus is a common genus of the three locations. Neighbor-joining cluster analysis showed that the endophytic bacteria of the three sampled flue-cured tobaccos were divided into 13, 9, and 11 groups. Comparing 9 phenotypic features by numerical classification indicated that the Wangqing and Helong strains gathered at the 7.2 level for 5 apparent groups, and the Yanji strains was clustered into 3 apparent groups at the 6.3 level. It provides a theoretical basis for the further application of endophytic bacteria of Jiyan 9.