Bacillus amyloliquefaciens SH-B10 isolated from deep-sea sediment produces two anti-fungal lipopeptides that were purified by bioactivity-guided fractionation based on acid precipitation, vacuum flash chromatography and semi-preparative HPLC. The two compounds were identified by tandem Q-TOF mass spectroscopy as C16 fengycin A (1) and a new fengycin with an aminobutyric acid at position 6 of the peptide backbone (2). Both compounds showed significant inhibitory activities against five plant fungal pathogens in paper-agar disk diffusion assay. This is the first report on the anti-fungal activities of the rare 6-Abu fengycin lipopeptides, and at the same time provided an insight into the potential of marine microbial resource in biological control and sustainable agriculture.