Abstract: The pot experiments were carried out to investigate the effects of bio-organic fertilizer on banana wilt disease and the influences of different fertilization treatments on bacterial community diversity in banana rhizosphere soil by Biolog-Eco plate method. The results showed that banana wilt disease was postponed by using bio-organic fertilizer. Control effects of bio-organic fertilizer on banana wilt disease were 55.4% after 30 days cultivation. The index of banana wilt disease was significantly negative correlated with AWCD in biolog plate, but significantly positive correlated with Simpson index. Results of principal components analysis indicated that distribution of different fertilization treatments were similar to the incidence trends, and rhizosphere microbial communities was obviously different; different fertilization treatments had a significant effect on the rhizosphere microbial community. Microbial activity in the rhizosphere soil of bio-organic fertilizer treatment was better. Furthermore, the category of carbon utilized by microbial in rhizosphere soil of bio-organic fertilizer treatment was different from that of organic fertilizer and control, and the polymers and amines were preferred.