Abstract: Anaerobic ammonium oxidizing (anammox) bacteria of phylum Planctomycetes origin have been identified to be responsible for N removal in terrestrial and aquatic environments through combined NH4+ oxidation and NO2 reduction. Anaerobic ammonium oxidation mediated by anammox bacteria has been noted to be a key process of biogeochemical N cycle in various ecosystems. It was also possible to have anammox processes in flooded paddy fields because of the low oxygen habitat conditions. To investigate the existence of anammox bacteria and the bacteria community diversity response to applied N fertilizer in paddy fields, anammox bacteria community structures in paddy fields were investigated with the aid of denaturing gradient gel electrophoresis and cloning sequencing by assay 16S rRNA gene in the third year of N fertilizer experiment in the field. DGGE images of 16S rRNA gene in surface or root-zone soil showed rich anammox bacteria in paddy soils. The numbers of DGGE band in the images of surface soil or root-zone soil under high N level treatment N3: 225 kg(N)·hm^-2 were greater than those under other N levels N2: 150 kg(N)·hm^-2, N1: 75 kg(N)·hm^-2 and CK: without fertilizer. The Shannon-Wiener index based on the number and density of DGGE band showed significantly (P < 0.05) higher diversity of anammox bacteria in surface soil or root-zone soil under N3 treatment than N2, N1 or CK treatments. At the same time, Shannon-Wiener index of anammox bacteria in surface soil was markedly (P < 0.05) higher than in root-zone soil under N3 treatment. Redundancy discriminate analysis (RDA) based on 16S rRNA gene DGGE profiles showed significant correlation (P = 0.006) of anammox bacteria community structure in surface soils of paddy fields with different levels of N fertilizer application. RDA plot depicted that anammox bacteria community structure in surface soil under N3 treatment obviously differed from that under N1 or CK treatment. Furthermore, 18 DNA sequences cloning from DGGE band was obtained and logged in GenBank. The findings demonstrated that anammox bacteria community structure in paddy soils strongly responded to intensive N fertilizer use especially in surface paddy soils. Anammox bacteria possibly played a critical role in N cycle in paddy soil ecosystem.