Abstract:[Background] Sclerotinia ginseng, one of the major pathogen attacking ginseng, seriously affects the yield of ginseng. [Objective] To explore the mechanism of ethyl acetate extract of the endophytic bacteria Endomelanconiopsis microspora from Taraxacum albiflos Kirschner & Štepanek in inhibiting S. ginseng. [Methods] The inhibitory effect was verified by the test of mycelial growth and spore germination of S. ginseng. The morphological changes of mycelia were observed under a microscope. The cell membrane permeability was detected by changes in conductivity and nucleic acid content, and the membrane lipid peroxidation was measured by changes in malondialdehyde (MDA) content and superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities. [Results] The ethyl acetate extract from E. microspora significantly inhibited the mycelial growth of S. ginseng with the minimum inhibitory concentration (MIC) of 3.75 mg/mL and the inhibition rate of 76.22% after 6 days of culture. The ethyl acetate extract significantly inhibited the spore germination of S. ginseng. The 15.00 mg/mL ethyl acetate extract demonstrated the optimal inhibitory effect with the inhibition rate of 90.69%. The ethyl acetate extract influenced mycelial morphology, increased cell membrane permeability of S. ginseng, and resulted in extravasation of mycelial inclusions. Compared with the control group, the treatment with 7.50 mg/mL ethyl acetate extract for 10 h increased the conductivity and nucleic acid content by 30.11% and 62.85%, respectively. At the same time, the ethyl acetate extract significantly increased MDA content and SOD, POD and CAT activities of S. ginseng. The MDA content and SOD, POD and CAT activities in the 7.50mg/mL treatment group first increased, peaked at the time point of 12 h, and then decreased. [Conclusion] The ethyl acetate extract from the endophytic bacteria E. microspora changed the cell membrane permeability of S. ginseng, aggravated the membrane lipid peroxidation, and destroyed the cell membrane integrity, thus leading to the loss of cell inclusions and inhibiting the spore germination and mycelial growth.