Reductive soil disinfestation (RSD) is an effective and environmentally-friendly method to suppress soil-borne pathogens. Real-time PCR and denaturing gradient gel electrophoresis were performed to investigate the influences of RSD on Fusarium oxysporum and soil microflora. Results showed that in 15 days after treatment, except for the NH₃ treatment, soil pH in Al-RSD and Et-RSD treatments decreased by 0.54 and 1.16 compared with that in the control treatment. NH₃, Al-RSD and Et-RSD significantly reduced the numbers of Fusarium oxysporum in soil by 76%, 98% and 94%, respectively. Al-RSD significantly increased the populations and diversities of bacteria. Al-RSD and Et-RSD significantly decreased the populations of fungi in the upper soil, but increased the fungal diversities. These results indicated that RSD has a better effect on the improvement of soil microflora compared with ammonia fumigation.