Technical Abstract: 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, with a long-term application of different fertilization treatments for 17 years. These 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 two molecular approaches, real-time quantitative PCR (QPCR) and denaturing gradient gel electrophoresis (DGGE), were used to study population structure of Fusarium spp. in the soils. Total genomic DNA of Fusarium from NF, NP and NPM treatments were 21.6, 40.6 and 514.5 pg 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 and NP treatments showed a significantly (P < 0.05) higher diversity index (H) and a significantly (P < 0.05) lower dominance index (C) than the NF treatment. Principal component analysis (PCA) indicated that the effect of NPM on soil population structure of Fusarium spp. was more obvious. The organic matter in the NPM treatment increased the abundance and diversity of Fusarium spp. in soil. Fertilization treatments might play a role in plant disease suppression by significantly affecting Fusarium populations in the soil.