Abstract: A total of 168 isolates with antagonistic effects against Phytophthora parasitica var. nicotianae (P. parasitica var.) were screened from 1000 endophytic bacteria isolated from flue-cured tobacco variety K326 at different growing stages, and bioassay results indicated that the inhibitory activities of these antagonists ranged from 12.54% to 50.14%. The biomass of endophytic bacteria was higher during the stages of seedling and rosette, which reduced by one order of magnitude during the stages of flowering and maturity; however, the number of antagonists kept an increasing trend. The RFLP analysis of 16S rRNA sequence on the 168 antagonists produced 10 RFLP patterns. Based on their RFLP patterns, 39 isolates were selected for 16S rRNA sequencing and phylogenetic analysis. The results showed that the 168 antagonists belonged to two groups of bacteria, namely Firmicutes and Actinobacteria, dominated by the genus Bacillus in Firmicutes group containing 6 RFLP patterns, 150 strains, including Bacillus amyloliquefaciens subsp. plantarum, Bacillus tequilensis, Bacillus methylotrophicus, Bacillus cereus, Bacillus thuringiensis and Bacillus aryabhattai. Bacillus amyloliquefaciens subsp. plantarum and Bacillus methylotrophicus emerged with the highest frequency. The remaining 18 strains belonged separately to 4 species, Brevibacillus formosus, Brevibacillus parabrevis, Pseudomonas umsongensis and Pseudomonas aeruginosa.