Community structures of ammonia-oxidizing bacteria and ammonia-oxidizing archaea in a red paddy soil were studied with aid of the denaturing gradient gel electrophoresis and DNA sequencing technologies Results show that ammonia-oxidizing bacteria and ammonia-oxidizing archaea in red paddy soil were in abundance. Changes in community structures of ammonia-oxidizing archaea were more acute than of ammonia-oxidizing bacteria. With the former, changes were observed between all four stages, while with the latter, only some were between the early growth stages (seedling and tillering) and the late growth stages (booting and maturing) of rice. Shannon-wiener index of ammonia-oxidizing bacteria did not vary much during the entire rice growth season, while Shannon-Wiener index of ammonia-oxidizing archaea increased significant with the succession of the rice growth stages, and leveled off at the booting stage. Potential nitrification rate of the soil rose sharply during the early rice growth period, peaked at the booting stage and then declined somewhat. The potential nitrification rate appeared to be in significantly positive correlation with the Shannon-wiener index of ammonia-oxidizing archaea, but not with that of ammonia-oxidizing bacteria. The findings demonstrated that the effects of ammonia-oxidizing archaea on nitrification of red paddy soil are more pronounced than ammonia-oxidizing bacteria, and both of them, especially archaea, play an important role in the composition of paddy soil microbes and the function of the ecosystem of red paddy soil.