Abstract: 【Objective】This study was aimed at screening antagonistic endophytic strains against stem rot in Jacaranda acutifolia, and investigating the antagonistic activity. 【Method】 Endophytic bacteria were isolated by dilution plating. F. chlamydosporum served as the test fungus, and antagonistic strains was obtained firstly by the five-point confrontation method and secondly by plate diffusion. Strains were identified by analyses of morphology and 16S rDNA sequence. Biocontrol effect was analyzed by greenhouse and field experiments. 【Results】The number of endophytic strains obtained was 24; the strain zhu66 with an inhibition rate of 97.8% was screened from the 24 strains. It was identified as Bacillus amyloliquefaciens by the 16S rDNA sequence analysis. Its GenBank accession number was JF899258. The greenhouse pot experiment showed that B. amyloliquefaciens could effectively prevent and treat stem rot in J. acutifolia. At a certain concentration, the higher the concentration, the better the anti-effect, and 10⁷ cfu/mL was at the optimal concentration.The control effect of sterilized soil was stronger than that of the natural soil. The control effect of the biocontrol strain inoculated before pathogen inoculation was stronger than that of the biocontrol strain and pathogen inoculated simultaneously; the control effect of pathogen inoculated before biocontrol strain inoculation was weak. It could promote growth of stems, and increase height and crown diameter of J. acutifolia. The higher the concentration, the stronger the effect. The field experiment further verified that the biocontrol effect on stem rot in J. acutifolia at different degrees showed remarkable differences. The preventive effect in the uneffective region was remarkably considerable,which had no stem rot. There was virtually no effect in the severely affected areas, although obvious control effect was observed in the mildly affected areas reaching 74.1%. There was a certain effect in the moderately affected areas, and with time, the control effect was enhanced.【Conclusion】B. amyloliquefaciens zhu66 strain could potentially serve as a biocontrol agent against stem rot.