Abstract: Community structures of ammonia-oxidizing bacteria and ammonia-oxidizing archaea in paddy soils of different rice cultivars were investigated by PCR denaturing gradient gel electrophoresis for soil DNA production. The results show that ammonia-oxidizing bacteria and ammonia-oxidizing archaea in paddy soils are rich, with more sorts in ammonia-oxidizing archaea than ammonia-oxidizing bacteria. The effect of rice cultivars on ammonia-oxidizing bacteria is strong. The community structures of ammonia-oxidizing bacteria are similar among the “TianA/Km71”, “Minyou1027” and “Km62/1027” rice cultivars, but different among the other three rice cultivars. Soil site effect on ammonia-oxidizing archaea is very obvious, with the highest differences in ammonia-oxidizing archaea community structures between bulk and rhizosphere soils of “TianA/Km71” and “Km62/1027” rice cultivars. The results demonstrate that different rice cultivars and soil site influence the community structures of ammonia-oxidizing microbial and ammomia-oxidizer, which, especially ammonia-oxidizing archaea, are important for the paddy soil ecosystems.