【Objective】 This study was conducted to investigate abundance and community structure of anaerobic ammonia oxidizing (anammox) bacteria in paddy soils under long-term fertilization and explore mechanism of anammox bacteria responding to different fertilizers, in an attempt to provide a scientific basis for rationalizing fertilization and understanding ammonia oxidizing processes in wetland ecosystems. 【Method】 Four treatments, i.e. control (CK), chemical fertilizer (NPK), chemical fertilizer plus cattle manure (NPKM), and chemical fertilizer plus straw (NPKS), were set in the field experiment of the study. Soil samples were collected from the treatments for analysis of abundance and community structure of soil anammox bacteria, using the fluorescent quantitative PCR assay targeting hydrazine synthase α-subunit (hzsA) gene and high-throughput sequencing technology aiming at 16S rRNA gene of anammox bacteria. 【Result】Significant differences were observed between the treatments in abundance of hzsA gene (p<0.05), exhibiting an order of NPKM>NPKS>NPK>CK. Correlation analysis (p<0.05) shows that abundance of hzsA gene was significantly and positively related to soil organic matter, total nitrogen and ammonia content. High-throughput sequencing shows Candidatus Brocadia, Candidatus Anammoxoglobus and Candidatus Scalindua were the main anammox bacteria and Candidatus Brocadia the dominant one in all the treatments. Bacteria diversity analysis shows that treatments CK and NPKS were significantly higher than treatment NPKM and NPK in Shannon index, Simpson index and Chao 1 index (p<0.05). 【Conclusion】 Long-term fertilization alters the anammox bacteria community in population and structure. The application of chemical fertilizers combined with organic manure is conducive to abundance of the anammox bacteria. However, the anammox bacteria community in the soil varies in structure with difference in fertilization. The anammox bacteria community increased in α-diversity in the soil applied with chemical fertilizer plus straw, but decreased in the soil applied with chemical fertilizer only and chemical fertilizer plus cattle manure. It can, therefore, be concluded that anammox bacteria vary in their response to different fertilizer or manure used in abundance and community structure.