[Aim] The invasion, expansion and spread of banana wilt disease (Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4)) in Yunnan province have led to serious threats to the stable banana industry and local farmer income. By analyzing the occurrence status of banana wilt disease in a seriously infected banana plantation, the prevention and control effects of different banana varieties and fertilization treatments on Fusarium wilt were identified, which provided a technical guideline for the prevention and control of this invasive disease.[Method] Field trials were set up using three treatments:shrimp peptide organic fertilizer + shrimp peptide special protection + shrimp peptide fruit Yekang (simplified as shrimp peptide organic fertilizer treatment), conventional organic fertilizer + microbial preparations (simplified as microbial treatment), and conventional organic fertilizer (simplified as control). Four different banana varieties of Brazilian, Guijiao No. 1, Nantianhuang, and Yunjiao No. 1 were evaluated for its resistance to TR4 in above three treatments. The disease incidence of TR4 in different fertilizer treatments and applied varieties was determined in four time periods during banana growth. The rhizosphere soil form the banana plantation was sampled for determination of pathogen content. The pathogen content in the soil was analyzed by real-time fluorescence quantitative PCR.[Result] The disease incidence of the four tested varieties in the three treatments varied. The disease incidence of Nantianhuang and Yunjiao No.1 was significantly lower than that of other two varieties. There was also a significant difference in disease incidence of the three treatments. The disease incidence from high to low was control > shrimp peptide organic fertilizer treatment > microbial treatment. The results indicated microbial agents could reduce the disease incidence of Fusarium wilt to certain content. The average monthly TR4 pathogen content in heavily infected banana plantation was more than 2000 copies; while the highest one reached 15148.9 copies.[Conclusion] Nantianhuang and Yunjiao No. 1 showed the highest disease resistance in field compared the two other varieties. However, further improvement of their resistance is needed before practical application is feasible.