Abstract: Banana Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense race 4, has been reported to be the most limiting factor in Cavendish-banana production worldwide since 1996. With the development of banana industry and regularization of produce in recent years, continuous banana cropping has become a common farming system. Furthermore, Cavendish-banana production comprises of about 90% of banana growing areas in south China, of which more than 200 000 hm2 banana orchards have suffered the disease. Among the management control of Fusarium wilt, rational crop rotation in combination with bio-organic fertilizer has been an effective and stable means of prevention of the disease. In this study, eggplant-banana rotation system was used to investigate the effect of cultivating eggplants combining bio-organic fertilizer on soil microflora in banana continuous cropping orchard with serious Fusarium wilt diseases using the plate count method and denaturing gradient gel electrophoresis (PCR-DGGE) technique. The chemical properties of the soil were also analyzed in the experiment. Results showed that the effects of application of bio-organic fertilizer on the number of culturable F. oxysporum, fungi and bacteria for both continuous cropping system and rotation with eggplant system of banana were not extremely significant compared with those of organic fertilizer treatment. However, compared with continuous cropping banana, rotation with eggplant of banana significantly reduced the number of culturable F. oxysporum, the number of culturable F. oxysporum decreased from 10⁴ cfu·g^-1 to 10³ cfu·g^-1 in dry soils. Despite no observed significant differences in soil physico-chemical properties between bio-organic fertilizer and organic fertilizer treatments of the eggplant-banana rotation system, soil pH, organic matter and available N, P and K contents increased under bio-organic fertilizer treatment. The ratio of bacteria to fungi (B/F) in eggplant-banana rotation system was significantly higher in bio-organic fertilizer than that in organic fertilizer treatment. Based on DGGE results, soil bacterial structure was obviously altered after eggplant-banana rotation with bioorganic fertilizer treatment for a year, and then soil bacterial richness, stability and diversity index increased compared with the control (continuous cropping of banana). The effect of eggplant-banana rotation system under bio-organic fertilizer treatment was good, and had a diversity index (Shannon-Wiener) of 3.22, while the control treatment with organic fertilizer had a diversity index of 2.89. In conclusion, the rotation of eggplant with banana could effectively improve soil microflora, and plus bio-organic fertilizer application even had a better effect.