Using real-time PCR and denaturing gradient gel electrophoresis (DGGE), effects of long-term fertilization on densities and structures of the soil microbial communities in corn fields of black soil were determined. The corn fields were located at the Hailun Experimental Station of Agricultural Ecology in Northeast China and had been under a long-term fertilization experiment designed to have 3 treatments, i.e. NF (no fertilizer), NP (chemical fertilizers nitrogen and phosphorus), and NPM (chemical nitrogen and phosphorus combined with pig manure). In real-time PCR analyses, the total genomic DNA of the microbial community in treatments NF, NP and NPM was found to be 381, 1351 and 1773 ng per gram of soil, and of the fungal community, 113.3, 127.3 and 20.6 ng respectively. Fungi to bacteria ratio in the 3 treatments was 0.31, 0.09 and 0.01, separately. Obviously Treatment NPM is lower than Treatments NF and NP in this aspect (p<0.05). Analysis of the DGGE indices shows that Treatments NP and NPM did not improve the soil microbial communities in diversity, uniformity and dominance of dominant microbes. However, according to principal component analysis, these two treatments altered the structures of the soil bacterial and fungi communities, especially the latter. Meanwhile, the tree clustering analysis indicates that the bacterial community structures in Treatments NP and NPM were quite similar, being 0.89 in similarity coefficient. But for the fungal community, its structure in Treatment NP is more similar to that in Treatment NF, with similarity coefficient being 0.63, which is higher than 0.51 between Treatments NP and NPM. All above findings indicate that the long-term fertilization using organic fertilizer (pig manure) could significantly decrease the fungal to bacterial ratio and alter the soil bacterial and fungal community structure in the filed.