Sixty strains of endophytic bacteria were isolated from the fruit of placenta of capsicum, and in antagonistic assay 13 of them showed antagonistic effect on Sclerotium rolfsii Sacc., the 6 most effective biocontrol strains also inhibited the growth of Phytophthora capsica and Colletotrichum capsici. Strain G242 and T443 were identified as Bacillus velezensis and strain YZ12, G241, T151, and T442 were verified as Bacillus amyloliquefaciens by 16S rRNA test. The planting experiments in the greenhouse were conducted on single strain or combining strains and the results indicated that the control effect of combining strains of G241 and T443 on Sclerotium rolfsii Sacc. reached to 88.41% which is much higher than G241(29.14%) and T443(38.16%) alone.