The invention discloses a composition which is prepared from riboflavin and bacillus subtilis Tpb55 in a ratio of (1.21-2.34):(97.76-98.79), and application of the composition in preventing and treating blackleg and brown spots of tobacco. When strains which are merely treated by bacillus subtilis Tpb55 are compared with those treated by the composition, the prevention and treatment effects on fungal diseases such as blackleg and brown spots of tobacco are remarkably improved, and the prevention and treatment effects are equivalent to those of main chemical medicines. The two components are good in compatibility, plant disease resistance induction substances for the prevention and treatment effects are increased, and the composition can be used as both bactericides and resistance inducers for preventing and treating fungal diseases such as blackleg and brown spots of tobacco after being compounded with biological microorganisms, and can be developed and used as a novel bactericide raw material.