Abstract:[Background] Root rot caused by Fusarium oxysporum is common in tobacco growing areas worldwide, severely threatening the quality and yield of tobacco. As chemical pesticides fail to effectively control the pathogen, biocontrol strains have attracted the interest of scholars. [Objective] To clarify the inhibitory effect of Bacillus velenzensis GDND-2 on the growth and development of F. oxysporium from tobacco. [Methods] The PDA containing 10% and 20% fermentation filtrate of GDND-2 was coated on glass slides, and then the conidia of F. oxysporum were inoculated. The effect of the fermentation filtrate on conidial germination, hyphal growth, sporulation, and pigment production of F. oxysporum was investigated, and the ultrastructure of F. oxysporum hyphae was observed by scanning and transmission electron microscopy. [Results] After the treatment with fermentation filtrate of GDND-2, the conidial germination was over 2 h late. The fermentation filtrate resulted in the malformation of germ tubes and early branching of hyphae. It inhibited the elongation of hyphae and thus they showed malformed spherical structure. The inhibition rates of hyphal growth by 10% and 20% fermentation filtrate were 53.41% and 61.58%, separately. The fermentation filtrate delayed the sporulation of the pathogen, significantly reduced the spore quantity, affected the conidial morphology, and promoted the pigment production by the pathogen. Under the action of 10% and 20% fermentation filtrate, the sporulation happened 20 h and 28 h late, respectively, and the inhibition rates of spore quantity were 52.11% and 78.85%, separately. The fermentation filtrate stimulated F. oxysporum to form microconidia. As for the ultrastructure of F. oxysporium, some hyphae swelled and malformed, with thinner cell wall, disappearance of cell membrane, cytoplasm exudation, and intracellular cavity structure. Some hyphae shriveled, twisted and thinned, and perforated in severe cases. Some hyphae cells were severely vesiculated and organelle distribution was uneven. In some cells, the number of liposomes increased obviously. [Conclusion] The fermentation filtrate of B. velenzensis GDND-2 inhibited the growth and development of F. oxysporum, including conidial germination, hyphal growth, and sporulation.