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Bacillus subtilis has a strong capacity of producing secondary metabolites and a predominant growth inhibition against pathogenic fungus.By the morphological, physiological and biochemical characteristics and 16S rDNA sequence analysis, we isolated a Bacillus subtilis HN09 from the rhizosphere soil of the neem tree.The HN09 strain was deposited at China General Microbiological Culture Collection Center (Accession No.CGMCC7524).Antagonistic experiments showed Bacillus subtilis HN09 has strong inhibitory effects against Fusarium oxysporum (92.4%), Fusarium oxysporum f.sp.radicis-lycopersici (90.5%), Colletotrichum higginsianum (86.3%), Magnaprothe grisea (82.4%), and Rhizoctonia solan (80.6%).A HN09 bioformulation was produced by inoculating and fermenting neem cake with the strain HN09 for 7 days.In the pot experiment, Fusarium crown and root rot in tomato plants was significantly reduced by application of HN09 bioformulation in soils.The disease incidence was as high as 94% in the control, while it was only 17% in HN09 bioformulation treatments.The bioformulation application also significantly promoted tomato growth.After30 days treatment with HN09 bioformulation, the plant height was 46.33cm, stem diameter 2.80cm, fresh weight47.43g, chlorophyll 52.63 spad, while the control plant height was 41.87cm, stem diameter 2.47cm, fresh weight of34.28g, chlorophyll 46.73 spad.Our study indicated integrated application of strain Bacillus subtilis HN09 and neem cake has a good potential to biocontrol Fusarium crown and root rot in tomato plants.