In order to discover high-efficiency biocontrol strain used to control the disease caused by Fusarium graminearum and reduce the agricultural economic losses, an antagonistic strain with anti-Fusarium graminearum rate 57.3% named Y-2 had been isolated from sea soil by plat confrontation method. It showed that Y-2 had high homologous to Bacillus amyloliquefaciens by morphology, physiological and biochemical characteristics, 16S rRNA sequence. The antifungal element of Y-2 had been further studied. The results showed that the element with antifungal activity was a lipid-peptide which located in the fermentation liquid and caused hypha swelling and spore germination delaying. It could inhibit another six plant pathogenic fungi and could biocontrol red mildew artificially infested with biocontrol rate 69.1%. These data would be helpful to offer a better biocontrol strain with antagonistic activity, and to provide basis to elucidate the antifungal mechanism.