The abundance and population structure of Fusarium spp. in field soils were assessed to determine the effect of different fertilization treatments on soil microbial community and potential role in disease management.The field was under soybean-wheat-corn rotation located in the black soil (Udic Mollisol) region of northeast China. Treatments included no fertilizer (NF), chemical fertilizers nitrogen and phosphorus (NP), and chemical nitrogen and phosphorus combined with pig manure (NPM). Soil samples were taken at the seedling stage of soybean and real-time quantitative PCR (QPCR) and denaturing gradient gel electrophoresis (DGGE) methods were used to study population structure of Fusarium spp. in the soils. Total genomic DNA of Fusarium from NF, NP and NPM treatments were 1.47, 2.33 and 56.79 ng per gram of soil as determined by the QPCR analyses. The quantity of Fusarium genomic DNA in NPM treatment was significantly higher (P <0.01) than in the other two treatments. According to the DGGE analysis, the NPM treatments showed a significantly (P<0.05) higher diversity index (H) and a significantly (P<0.05) lower dominance index (C) than NP and NF treatments. Principal component analysis indicated that soil population structure of Fusarium spp. in the NPM treatment was more diversified. Severity of root rot on soybean was significantly lower when the plants grew in field soil with NPM treatment compared with the other two treatments. The results indicated that fertilization treatments might play a role in plant disease suppression by significantly affecting Fusarium populations in the soil.