BACKGROUNDAs a highly prevalent epidemic disease of potato, late blight caused by Phytophthora infestans poses a serious threat to potato yield and quality. At present, Chemical fungicides are mainly used to control potato late blight, but long‐term overuse of chemical fungicides may lead to environmental pollution and human health threats. Endophytes, natural resources for plant diseases control, can promote plant growth, enhance plant resistance, and secrete antifungal substances. Therefore, there is an urgent need to find some beneficial endophytes to control potato late blight.RESULTSWe isolated a strain of Bacillus subtilis H17‐16 from potato healthy roots. It can significantly inhibit mycelial growth, sporangia germination and the pathogenicity of Phytophthora infestans, induce the resistance of potato to late blight, and promote potato growth. In addition, H17‐16 has the ability to produce protease, volatile compounds (VOCs) and form biofilms. After H17‐16 treatment, most of the genes involved in metabolism, virulence and drug resistance of Phytophthora infestans were down‐regulated significantly, and the genes related to ribosome biogenesis were mainly up‐regulated. Moreover, field and postharvest application of H17‐16 can effectively reduce the occurrence of potato late blight, and the combination of H17‐16 with chitosan or chemical fungicides had a better effect than single H17‐16.CONCLUSIONOur results reveal that Bacillus subtilis H17‐16 has great potential as a natural fungicide for controlling potato late blight, laying a theoretical basis for its development as a biological agent.This article is protected by copyright. All rights reserved.