The antagonistic strain Bacillus amyloliquefaciens strain S13-3 decreased the severity of strawberry anthracnose caused by Colletotrichum gloeosporioides. The foliar application of S13-3 triggered the expression of pathogenesis-related proteins, chitinase and β-1,3-glucanase, in strawberry leaves. We identified lipopeptide antibiotics, including iturin A, fengycin, mixirin, pumilacidin and surfactin, produced and secreted by S13-3. Iturin A and surfactin elicited the gene expression of the pathogenesis-related proteins in strawberry leaves, suggesting that antagonistic strain S13-3 confers resistance to strawberry leaves through the production of lipopeptide antibiotics. In fact, iturin A and surfactin triggered induced systemic resistance on strawberry plants, resulting in the reduction of the severity of anthracnose disease caused by Colletotrichum gloeosporioides. The bifunctional activity of S13-3, which consists of the antagonistic effect and the induction of plant defence response by the antibiotics produced by it, may make S13-3 an innovative biological control agent against phytopathogens in strawberry. This study tries to determine whether biocontrol of phytopathogens by Bacillus amyloliquefaciens in strawberry can be connected to induced plant resistance. The results suggested that the antagonistic strain B. amyloliquefaciens S13-3 confers resistance to strawberry through the production of lipopeptide antibiotics.