The discovery of the complete ammonia-oxidizing microbes, Comammox , had fundamentally changed our perspective on traditional nitrification. The microbe also played a potentially under-appreciated role in the biogeochemical N cycle and provided a new dimension for the research of nitrification. To investigate the abundance of Comammox in different ecosystems was urgently needed. In the present study, three treatments with different quantities of fertilization in a paddy soil (blank control, NPK and 1.5 NPKS) to investigate the nitrification and gene abundance for nitrifying microorganisms, especially for the complete ammonia oxidizing bacteria (Comammox ). The results showed that:① Both Comammox Clade A and Comammox Clade B were detected in all three treatments, and the abundance of Comammox Clade A were 9.0×10, 1.7×10, 7.2×10 copies·g (dry soil), respectively, and for Comammox Clade B were 1.5×10, 1.2×10, 1.7×10 copies·g (dry soil), respectively. ② The abundances of both ammonia-oxidizing archaea (AOA)in the three fertilizers was 1.5×10-1.2×10 copies·g (dry soil), and the ammonia-oxidizing bacteria (AOB) in the three fertilizers was 2.0×10-9.3×10 copies·g (dry soil), lower than the abundance of the Comammox. The ratio of Comammox to AOA was 7.2, and the ratio for Comammox to AOB was 524.4 for blank control, were greater than NPK and 1.5 NPKS treatments. ③ The ratio of Comammox Clade A to Comammox Clade B showed an increasing trend with the increase in fertilizer application, at 6.1, 14.4 and 43.1, respectively. ④ For NPK and 1.5 NPKS treatments, Comammox Clade A gene copies were 1.9 and 8.0 times higher than that of the blank control treatment respectively, and the numbers for AOA significantly increased to 3.2 and 7.2 times that of the blank control. The AOB gene copy numbers increased by two orders of magnitude compared with the blank control. In addition, the nitrification potential increased with the increase in N fertilizer application; however, the effects of different fertilizer treatments on Comammox Clade B were not significant. Results indicated that Comammox was widely distributed in the neutral purple paddy soil and was higher in abundance than AOA or AOB, which implied that Comammox-especially Clade A-may contribute to the nitrification of paddy soil.