Anthracnose caused by Colletotrichum spp. is a well-known disease that causes severe losses in pepper production which is used as a spice for thousands of households in many parts of China. With the biological control properties of endophytic strains have been developed and used have been of great importance in the prevention and control of anthracnose and environmental protection. Therefore, to control the pathogen Colletotrichum scovillei more safely, 58 endophytic strains were isolated from pepper leaves in this experiment. Plate resistance method was used to screen the antagonistic strains of C. scovillei, and it was found that the inhibition rate of 25 antagonistic strains against C. scovillei was greater than 60%, and the inhibitory rates of L1-7 and L3-5 against it were 79% and 80%, respectively. They were identified as Bacillus amyloliquefaciens and Bacillus velezensis by culture and morphological identification, combined with 16S rDNA and gyrB gene sequence analysis. The two antagonistic endophytic bacteria also had the ability to fix nitrogen and secrete IAA, and all had high salt tolerance. Controlled pot experiments in the laboratory showed that L1-7 and L3-5 had a good control effect against C. scovillei, with the control efficiency reaching 80.64% and 73.39%, respectively. Thus, B. amyloliquefaciens (L1-7) and B. velezensis (L3-5) could be useful as biological control agents to protect peppers from anthracnose disease caused by C. scovillei. The results of this test provide a basis for the development of pepper endophytic bacterial resources, and also bacterial resources for the biological control of C. scovillei.