The abundance and composition of ammonia oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated from two long term field fertilization experiments (upland red soil and red paddy soils respectively) using quantitative real-time polymerase chain reaction,denaturing gradient gel electrophoresis (DGGE) and constructing clone library based on amoA genes.The soil samples used in this study were collected from the Ecological Experimental Station of Red Soil,Chinese Academy of Sciences,located at Yingtan,Jiangxi Province,China.The long-term fertilizer experiment for upland soil was established with nine treatments including 3 replicates in a randomized plot design:control without fertilizers (CK); chemical fertilizer nitrogen (N); phosphorus (P); potassium (K); combinations of chemical fertilizers NP ; NK ; NPK; 2NPK; and NPK + organic manure (OM).The long-term fertilization experiment for red paddy soil had one more treatment with only organic matter (OM).AOA amoA gene copies outnumbered AOB in all samples.