Abstract: The effects of temperature on the structure of nitrifying bacteria in A²/O system were studied for the purpose of technique improvements and system regulations. Total microbial DNA was extracted from samples which were collected from reactor, then target DNA fragments were amplified from the total DNA using specific bacterial primer. The target DNA were used for denaturing gradient gel electrophoresis(DGGE) analysis. Results indicated that the changes of temperature could affect the community structure and the Shannon diversity index of nitrifying bacteria. The structure of AOB community was stable when the temperature was higher than 25 ℃, the removal rate of NH₄^+-N was over 95% in this condition; The structure of Nitrobacter community was stable when the temperature was higher than 20 ℃, the removal rate of NH₄⁺-N can reach 95% in this condition; The structure of Nitrospira community changed greatly when the temperature changed, comparatively speaking, the community structure was most stable when the temperature was between 15 ℃ to 20 ℃, the removal rate of NH₄⁺-N was between 75% to 95% in this condition.