This study investigates the efficacy of short peptides secreted by Bacillus subtilis for fungi inhibition and shelf-life maintenance of fresh-cut pumpkin.Low-molecular-weight filtrate (LC< 1,000 Da) of B. subtilis culture (BC) significantly lowered the total number of moulds on fresh-cut pumpkin compared with the untreated control and BC group after storage. LC prevented the deterioration of sensory quality in pumpkin incision, and reduced pectinase activity. LC also inhibited the growth of Phytophthora capsici and Penicillium chrysogenum, and the activity of β-1,3-glucan synthase (GS) secreted by both moulds. Fifty-seven GS-inhibiting peptides were screened from 95 LC peptides with 2-5 amino acid residues. The two most potent peptides, AWYW and HWWY, had highly suppressive effects on the growth of P. capsici and P. chrysogenum.Our study demonstrated that short peptides present in Bacillus subtilis culture can play an important role in the maintenance of fresh-cut pumpkin by suppressing fungal growth. This article is protected by copyright. All rights reserved.