Abstract:[Objective] Antagonistic endophytic bacteria against Monilinia fructicola were screened from the roots of peach trees. The inhibitory mechanism was studied at cellular level. [Methods] The confront-culture method was adopted to screen endophytic bacteria against M. fructicola. The obvious features of antagonistic strains were determined by cell morphological observation, physiological and biochemical characteristics. Strains were identified by 16S rRNA gene sequencing and phylogenetic analysis. The effect of biological control was tested through the experiment of fruits in vitro. The change of mycelia, spore morphology and the internal structure of cells was observed under electron microscope. [Results] By secondary screening, three strains had obvious and stable effect antagonist M. fructicola, these strains were identified as Bacillus subtilis. The experiment of fruits in vitro showed that the three strains inhibited the growth of M. fructicola obviously. Results of microscopic analysis show that the mycelia inhibited by the antagonistic bacteria were obviously attenuated, with severe disorder, twining and knotting. Most spores were shriveled, enlarged and rupture. In cells of the pathogen inhibited by the antagonistic bacteria, the phenomena of cytoplasm exosmosis, protoplast shrinkage and condensation, and a large amount of cavities were observed. [Conclusion] The three strains of the endophytic bacteria screened from the roots of peach trees had effective inhibitory on the growth of M. fructicola, these strains could be served as new resources against M. fructicola.