Anthracnose, caused by Colletotrichum species, inflicts severe economic losses on agricultural crops. This study investigated C16 Fengycin B from a deep-sea Bacillus strain against Colletotrichum fioriniae. Our findings demonstrated that C16 Fengycin B effectively inhibited fungal growth, with a minimum inhibitory concentration (MIC) of 32 μg/mL. Microscopic analysis revealed that treatment with C16 Fengycin B caused hyphal swelling and thickening of cell walls. Transcriptomic analysis suggested that the primary antifungal mechanism affected critical fatty acid pathways, with reduced efficacy in a mutant lacking fatty acid pathway genes. Biochemical analyses showed C16 Fengycin B induced accumulation of glycerol, free fatty acids, and reactive oxygen species (ROS). Furthermore, in situ assays confirmed its effectiveness in controlling anthracnose in pear fruits. This study reveals a novel antifungal mechanism whereby C16 Fengycin B inhibits the growth of C. fioriniae by interfering with fatty acid pathways, highlighting its potential as a biocontrol agent for managing anthracnose.