267 endophytic bacteria of tobacco were isolated from roots, stems and leaves by the method of grinding separation. A preliminary analysis was made on the diversity of the isolates by phenotypic characteristics and molecular classification methods based on partial 16S rDNA sequences, the analyti-cal comparison was also made between them. 267 bacteria isolates were separated with 8 different phenotypic characteristics, and were grouped into 5 clusters and 56 subclusters at the level of 2.15 with numerical classified based on the unweighted pair group method with arithmetic averages algorithm, and they were clustered into 21 molecular groups based on partial 16S rDNA sequences. The results show that there are much more phenotypic types than molecular groups, phenotypic characteristics was not consis-tent with the results of molecular classification exactly. The result of sequence analysis of the 16S rDNA showed a 98%?99% homology with 21 species in the GenBank. The dominant bacterial groups of to-bacco endophytic bacteria belong to Firmicutes, Bacillus genera.