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Sclerotinia rot infected by cosmopolitan fungi Sclerotinia sclerotiorum is a serious and destructive disease in carrot production, especially during their postharvest storage. Natural products with the advantages of environmentally friendly and safety have been widely concerned. This research estimated the impact of hinokitiol against S. sclerotiorum and on the quality of carrots. In vitro and in vivo tests demonstrated that hinokitiol had promising antifungal activities against both carbendazim-susceptible and -resistant isolates of S. sclerotiorum. Importantly, it effectively kept the quality and prolonged the shelf life of carrot by declining the loss of weight, ascorbic acid, carotenoid, and total phenolics content, preventing the formation of malondialdehyde, and enhancing the activities of antioxidant enzymes. Further study found that hinokitiol inhibited the formation of sclerotia by destroying the morphology and the integrality of cell membrane, reduced the pathogenicity by suppressing the synthesis of oxalic acid and exopolysaccharide, declined the activities of enzymes and the gene expression related to sclerotia development in S. sclerotiorum. These information evidenced the great potential of hinokitiol as a natural fresh-keeping agent for the management of postharvest decay infected by S. sclerotiorum. • Hinokitiol had promising antimicrobial activities against S. sclerotiorum. • It maintained the quality and extend the shelf life of carrots. • It inhibited the myceliogenic and carpogenic germination of sclerotia. • Hinokitiol prevented the development of sclerotia might the main action mechanism. [ABSTRACT FROM AUTHOR]