The use of biocontrol agents decreased the stress indicator enzymes and malondialdehyde content by 55–70% and 62%, respectively as compared to control. The denaturing gradient gel electrophoresis (DGGE) analysis showed significant variations in the fungal and bacterial community structures of all treatments resulted from UPGMA cluster analysis. This study showed that S. goshikiensis YCXU could be a potential biocontrol agent for controlling watermelon Fusarium wilt disease.