[Objective] To provide candidate strains and effective strategies for the control of mulberry fruit sclerotiniose, we screened out the endophytic bacteria with biocontrol potential for mulberry fruit sclerotiniose from a resistant mulberry cultivar. [Methods] The endophytic bacteria antagonistic to mulberry fruit sclerotiniose were isolated from mulberry plants by the tissue culture and confrontation culture methods. The antagonistic strain was identified based on morphological features, physiological and biochemical characteristics, and the phylogenetic relationship based on 16S rRNA gene sequences. The antimicrobial spectrum and control efficiency to detached mulberry fruits were determined to evaluate the application potential of the antagonistic strain. Furthermore, we observed the inhibitory effect of the fermentation supernatant of the strain on the mycelial growth of the pathogen, measured the variations in glycogen and reactive oxygen species accumulation of the pathogen treated with the antagonistic strain, and determined the expression of pathogen-related genes after treatment with the antagonistic strain to decipher the antagonistic mechanism of this strain. [Results] An endophytic bacterial strain C1R32 with strong and stable antagonistic activity on Sclerotinia sclerotiorum PZ-2 (the pathogen of mulberry fruit sclerotiniose) was isolated from a healthy mulberry branch. C1R32 showed similar morphological features and physiological and biochemical characteristics with Bacillus. The phylogenetic analysis based on 16S rRNA gene sequences revealed that C1R32 was located in the same clade with B. subtilis. Therefore, strain C1R32 was identified as B. subtilis. B. subtilis C1R32 had antagonistic activities against a variety of phytopathogens including S. sclerotiorum. The suspension and fermentation supernatant of B. subtilis C1R32 showed the control effects of 52.94% and 46.43%, respectively, on sclerotiniose of detached mulberry fruits. The cell-free fermentation supernatant of B. subtilis C1R32 caused the hypha swelling and distorting, cell wall breaking, and cytoplasm leakage of S. sclerotiorum PZ-2. Moreover, B. subtilis C1R32 inhibited S. sclerotiorum PZ-2 by reducing glycogen accumulation, promoting reactive oxygen species burst, and influencing the expression of genes associated with antioxidant activity. [Conclusion] We isolated an endophytic B. subtilis strain capable of controlling mulberry fruit sclerotiniose from a resistant mulberry cultivar and preliminarily explored its antagonistic mechanism, providing potential strain resources for the biocontrol of mulberry fruit sclerotiniose.