Abstract: Effects of long-term application of N, NP, NPK, M (pig manure), and MNPK (pig manure plus NPK) on soil microbial carbon (SMB-C), soil microbial nitrogen (SMB-N), and ammonium oxidizing bacterial (AOB) diversity in a paddy soil derived from yellow-brown earth in Hubei Academy of Agricultural Sciences were studied. Results showed that, all fertilizer treatments tended to increase soil organic matter, total N, SMB-C (N), and alter the AOB community compared with the control. Among the six treatments, MNPK acquired more complex AOB community structure than those of chemical fertilizers application only. Unweighted Pair Group Method Clusting (UPGMC) analysis of the DGGE banding patterns showed that, treatments harvesting rice and wheat were divided to two classes respectively. After the same crop harvested, all treatments were divided to two classes. M and MNPK were grouped into one class, and N, NP, NPK and CK were clustered into the other. And there were difference between rice and wheat harvested in the latter class. Sequence analysis of prominent bands in DGGE profiles showed that Nitrosospira and Nitrosomonas within -proteobacteria were the dominant ammonium oxidizing bacteria in studied soil.