Abstract: Nitrification is an essential process in agricultural ecosystems. The classical two-step nitrification, the oxidation of ammonia to nitrate via nitrite, is radically challenged by the recent discovery of complete ammonia oxidation (comammox). The first and rate-limiting step of nitrification, ammonia oxidation is mainly performed by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) which carry the ammonia monooxygenase (amoA) gene. The first report of comammox has triggered many scientific issues and deeply thoughts concerning physiology, distributing characteristic, relative contributions of comammox to nitrification since 2015. Here, current knowledge of differences in the discovery, phylogeny and environmental responses between AOB, AOA and comammox were summarized, in order to significantly improve our fundamental understanding of nitrogen transformation in agricultural soils, and to provide important scientific evidence for nitrogen fertilizer management, thus helping mitigate agricultural non-point pollution and nitrous oxide emissions.