Soil-born diseases mainly caused by continuous cropping of monocultures are world-wide problems and seriously restrain the development of contemporary agriculture. Traditionally, farmers use chemical pesticides as a relatively dependable method of protecting plants from soil-borne pathogens. However, increased use of chemical pesticides have several negative effects on the environment and human health and restrictions have increased on use of a variety of chemical pesticides. Therefore, there is an urgent need for effective and environmentally friendly ways to prevent and control soil-borne diseases. Banana fusarium wilt caused by Fusarium oxysporum f. sp. Cubense (FOC) is a kind of world-wide soil-borne diseases and causes serious economic loss every year. The effective ways to prevent the disease are still not available. The experiment was carried out in October 2012. The study site was located in Ledong, Hainan province, China (18°65' N, 107°79' E). The filed used in the experiment was planted with banana for many years, and had a high Fusarium wilt disease incidence of more than 50%. The experiment contained ten treatments, i.e. (1) untreated soil, (2) disturbed soil, (3) flooding disturbed soil, (4) flooding soil incorporated with rice straw at low rate, (5) flooding soil incorporated with rice straw at high rate, (6) flooding soil incorporated with rice straw at high rate plus lime, (7) flooding soil incorporated with pig manure, (8) flooding soil with bagasse, (9) flooding soil with bagasse plus lime, and (10) flooding soil with lime. The soil pH, contents of SO₄^2-, NO₃^- and NH₄⁺, and the populations of bacteria, actinomyces, fungi and FOC of the soils were analyzed at 5, 10, and 15 days after flooding and drained. The results showed that the soil pH in the flooding treatments were raised in the fifth day significantly compared with untreated soils and then became gradually declined over treated time. The contents of SO₄^2- and NO₃^- were decreased significantly, while the content of NH₄⁺ were increased in the soils with straw, pig manure and lime, respectively, under flooding conditions. Flooding the soil incorporated with organic matters significantly reduced the populations of cultivable actinomyces and fungi but not influenced the populations of cultivable bacteria. The populations of FOC were significantly declined in the soils with increasing the rate of incorporated rice straw under flooding condition to 2.88% of untreated soil. Incorporation of bagasse and lime decreased the population of FOC significantly as well, but less effectively than with rice straw did under flooding conditions. Pig manure was not effective to reduce the FOC population. The total amounts of microbe in the treatments applied with organic matters were raised compared with untreated soil. These resluts indicated that anaerobic conditions created by flooding soil incorporated with organic matters not only reduced the FOC population in the soil, but also improved the soil physicochemical properties and microbial communities. It is the first report in China that quickly and intensively anaerobic conditions created by flooding soil incorporated with organic matters effectively reduce the population of plant pathogens within 15 days. Therefore, anaerobic soil disinfection would provide a feasible measure for the control of banana fusarium wilt in agricultural production. Furthermore, the method provides a way to recycling use of crop residues.