In order to screen ecological fumigants for ensuring banana sustainable cultivation in monoculture banana planting orchard, the effects of fumguation with different chemical compounds on the numbers of Fusarium oxysporum f. sp. cubense race 4 (FOC) in water and banana orchard soil and on soil microflora were studied using the traditional plate-counting method combined with polymerase chain reaction denaturing gradient gel electrophoresis (DGGE) in this study. Fumigants included lime, ammonium bicarbonate, the mixture of lime and ammonium bicarbonate, chlorine dioxide, sodium hypochlorite, hydrogen peroxide and ammonia water. Results showed that all kinds of fumigants above can kill the spores of FOC in the water, while in soil, ammonia water and the mixture of lime and ammonium bicarbonate showed more effective antifungal effect than other fumigants. Thus, these two kinds of fumigants were selected for further study. Experiments of different dosages of ammonia water and the mixture of lime and ammonium bicarbonate in pot soil showed that the higher dosage of fumigants added, the better antifungal effect. Both the two kinds of fumigants decreased the culturable bacteria and fungi amounts, and the decline for bacteria was significantly lower than the fungi. As shown in DGGE, fungal bands were more influenced compared to the bacteria regardless of fumgation with ammonia water or the mixture of lime and ammonium bicarbonate, indicating the rapid decrease of abundance for fungi. While for bacteria, some bands appeared and some bands disappeared. Furthermore, compared with the control, the indexes of richness, evenness, stability and diversity of total bacteria amended with different dosages of fumigants were all decreased and the indexes were highest in sample treated with 2.67 ml/kg of ammonia water or 3.33 g/kg of lime mixed with 1.67 g/kg of ammonium bicarbonate among the two group treatments. In conclusion, all the results show all the chemical compounds could be used as fungicide in the water and confirm that not only ammonia water with the best additive amount of 2.67 ml/kg but also the mixture of lime and ammonia bicarbonate (3.33 g/kg and 1.67 g/kg, respectively) can be used as fumigants in soil.