Fusarium Head Blight (FHB) is economically one of the most important fungal diseases of wheat in the world. The aim of this research was to determine the antifungal effects and metabolites of native Bacillus species. Bacillus strains isolated from soil of fields grown wheat and barley, exhibited in vitro and in vivo antagonism against some Fusarium species isolated from infected wheat seeds. An attempt was made to partially purify and characterize the diffusible antifungal metabolite/s produced by the selected Bacillus strain. High Performance Liquid Chromatography (HPLC) of partially purified extract showed the presence of lipopeptide antibiotic iturin as a major peak that was comparable to that of standard iturin A(11.80 min) from Sigma–Aldrich. The structure was further confirmed by Fourier Transform-Infrared Spectrum(FTIR) and Liquid Chromatographic Mass Spectrometric(LCMS) analysis asiturin A. LCMS analysis also showed the presence of fengycin beside siturin A. The genome of the selected isolate of Bacillus had shown 99.9 percent similarity by B. aryabhattai and the genome of the selected isolates of Fusarium had shown 99 percent similarity by F. graminearum. The antifungal effects of Bacillus strains in the glasshouse conditions was also confirmed. Disease severity in plants inoculated with the pathogen and Bacillus strains was significantly less than the pathogen control. According to the results of this experiment, the antifungal effects of native Bacillus strains and also their effects in the biological control of wheat FHB disease were confirmed.