By tissue separation, endophytic bacteria with anti-anthrax activity were screened from healthy capsicum fruits in Hengyang area of Hunan Province, and one strain named C3 with strong antagonistic effect against anthrax in capsicum was selected from 100 endophytic strains. The inhibition bandwidth of strain C3 aganist the pathogen of capsicum anthracnose in the confrontation test on a plate was 16.5 mm, and the inhibition rate reached 80.26%. Based on physiological-biochemical and molecular identification, strain C3 was identified as Bacillus velezensis. The lesion was the smallest when strain C3 was applied at bacterial concentration of 1.0×107 cfu/mL in fruit infection test. In the indoor pot experiment, the control effect against anthracnose reached 90.67% when spraying 50 mL/per plant with strain C3 bacterial solution at a concentration of 1.0×107 cfu/mL, and the control effect was still 68.64% with bacterial solution at a concentration of 1.0×106 cfu/mL. Field plot experiments showed that the control effect reached 48.71% when spraying 2 L in each plot with strain C3 bacterial solution at a concentration of 1.0×107 cfu/mL, which was close to that(54.18%) of chemical control with 400 mg/L pyraclostrobin.