Anaerobic ammonium oxidation (anammox) bacteria and ammonia oxidation archaea (AOA) play a very important role in nitrogen cycle in soil as well as in the marine ecosystems. These excellent discoveries have renewed the vision on nitrogen cycle. Anammox uses nitrite as an electron acceptor to convert ammonium into dinitrogen gas. The nitrite is delivered by AOA, since they convert ammonia into nitrite. To further explore this view, the coexistence of anammox bacteria and AOA bacteria were also studied in deep soil and paddyfield wetland using molecular and isotopic tracing tools. For the detection of anammox bacteria, primer combination AMX 368F and AMX 820R was used, whereas for AOA the archaeal primer set for amoA gene was used. Four different anammox bacteria and five different AOA were detected in the deep soil layer of high nitrogen loaded paddyfield. Further analysis showed that the biodiversity of anammox bacteria was low, 35 sequences of anammox bacteria were assigned to 4 Operational Taxonomic Units (OTUs), three of them close to the known anammox species derived from marine and wastewater treatment plant except the OTU4, which clustered with Candidatus ‘Kuenenia stuttgartiensis’ with a high similarities up to 95%. 20 sequences of AOA were assigned into 5 OTUs, and the similarities with the closest relatives in GenBank were mostly higher than 98%. 4 of the OTUs belong to the water/sediment lineage and another one OTU was close to the soil/sediment lineage. This character of AOA diversity was also corresponded to the nature properties of wetland soil which fall in between soil and freshwater environment. The isotopic tracing experimental results showed that the ratio of N2 production by anammox to total (anammox denitrification) ranged from 24.1 to 29.8 percent. This is the first report which prove the anammox process in deep soil layer of paddyfield wetland by both molecular and isotopic tracing tools. AOA probably play an important role in ammonia oxidizing because its wider ecologic niche than other ammonia oxidizing microorganisms. Whether nitrification driven by bacteria or archea is still in debate so far. However, in this study, an anaerobic and ammonia affluent environment which is not fond of ammonia oxidizing bacteria was provided. The strong anammox activity implied that the nitrite which was oxidized by AOA should be one of an important sources supplies for anammox process. In consideration of the nitrite supplied by denitrification, therefore, how much it plays in the nitrite supply for anammox process by AOA? We are looking forward to the appearance of a more powerful experimental tools. Anyway, it provided a new idea of the widespread of anammox process with the prove of the coexistence of anammox and AOA in this special environment.