Abstract: Two Lysine Bacillus and Stenotrophomonas strains were previously selected from exudates of flue-cured tobacco to be able to depredate effectively nicotine, salicylic acid and other secretions. A mixture of 5ml bacterial suspension and 45mL secretions was added into the seedling trays to test their effects on flue-cured tobacco seedling photosynthetic characteristics, chlorophyll fluorescence characteristics, chlorophyll content and root growth. The results showed that the exudates containing degrading bacteria could improve photosynthesis during the process of seedling growth, and promote the growth of root. The degradation effect of flue-cured tobacco root exudates containing both Stenotrophomonas Bacillus andLysine bacteria was the best, followed by the degradation solution that only contained Lysine Bacillus or Stenotrophomonas strains, and that the treatingsolution without degrading bacteria inhibited the growth of flue-cured tobacco seedlings. In the pot experiment, both bacteria were capable of reducing the inhibition of tobacco growth by root exudates, with the best effect observed when both bacteria wereused.