Abstract: 【Objectives】 Ammonia-oxidizing archaea (AOA) plays an important role in the nitrification process. To investigate the effects of long-term fertilization on nutrients, abundance and community structure of AOA in soils, a filed experiment was performed to evaluate the optimum fertilizer mode. 【Methods】 The long-term fertilization experiment was started in 1983 in red paddy soil in Fuzhou City,Fujian Province. Four fertilization treatments with three replicates were designed as described in the following expression: No fertilization (CK); NPK, NPKM (NPK combining manure) and NPKS (NPK combining straw), and each plot of treatments was set by 12 m2. Soil samples were collected after harvesting rice in October, 2012. Nutrient contents in soil were measured, and the abundance and community structure of ammonia-oxidizing archaea (AOA) in paddy soil were determined using real-time PCR and clone library. 【Results】 1) Compared with the control, the NPKM and NPKS treatments significantly increased the content of soil organic matter, but no significant differences were observed between theses two treatments. 2)Relative to the control, application of fertilizer could increase the content of soil total nitrogen. NPKM and NPKS treatments increased the content of total phosphorous in soil. NPKS treatment increased the content of total potassium in soil. 3) Long-term fertilization increased the contents of soil available nitrogen (AN), available phosphorous (AP) and available potassium (AK), and the NPKM treatment exhibited the highest contents of available N and P, and the highest content of available K was demonstrated in the NPKS treatment. 4)Long-term fertilization had no effect on the soil pH. 5)NPKM and NPKS treatments increased AOA abundance comparing to the control, and NPKM treatment had the highest population size of AOA, but there was no significant difference in population size of AOA between the NPK treatment and the CK, and a significant positive relationship was observed between AOA abundance and the soil organic matter content (P0.05), and there was significantly positive relationship between TP, AN, AP, AK and AOA abundance (P0.01). 6)Long-term fertilization changed the community structure of AOA in soil. Chemical fertilizer increased the diversity indices of AOA. However, chemical fertilizer combining organic fertilizer decreased the diversity indices of AOA in soil. 7)All AOA sequences belonged to uncultured archaea such as Crenarchaeota and Thaumarchaeota. Most of AOA come from the soil and sediment lineage. 【Conclusions】 Combination application of chemical fertilizer and organic fertilizer increased the contents of organic matter, nutrients, the abundance of AOA and the ratio of the predominant AOA in soil.