Abstract: Fusarium and Alternaria are two kinds of common pathogenic fungi which can cause tree diseases, especially harmful to nursery plants, and may lead to serious economic loss. Biological control is a promising and environmentally friendly method to control the phytopathogens. Bacillus velezensis FZB42 strain is a plant growth promoting rhizobacterium with potent biocontrol activity. To explore the spectrum of its antagonistic activity, we tested the effect of FZB42 on two fungi species, Fusarium solani and Alternaria tenuis. The results showed that FZB42 could inhibit the growth of both of the species. Further, we constructed three FZB42 mutants(ΔbmyA, ΔfenA and ΔbmyAΔfenA)via homologous recombination. Using the three mutants we demonstrated that bacillomycin D and fengycin synthesized by FZB42 are important to inhibit the growth of the fungi, and the two antagonistic molecules have significant synergistic effect.