Abstract To extend the storage period and shelf life of Morchella and reduce environmental pollution problems, in this experiment, pathogenic fungi were isolated and identified from the naturally-occurring Morchella, and the antibacterial activity of 22 kinds of plant essential oils was determined by the plate dilution antibacterial method. The results showed that a strong pathogenic fungus strain YDJ-P was isolated and identified from the naturally-occurring Morchella, and it was identified as Rhizopus stolonifer based on morphology and molecular biology. The antibacterial activity of 22 essential oils showed that the essential oils of Clove, Styrax and Spearmint had obvious inhibitory effect on the strain YDJ-P, and the inhibitory rate was 100 % at a concentration of 1000 μl/L. The bacteriostatic rate of Patchouli, Inula, Oregano, Neroli and Myrrh essential oils against strain YDJ-P were significantly different from that of completely bacteriostatic essential oils (P < 0.01), all >50%.