The roles of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), as drivers of ammonia oxidation, in nitrogen cycle have been one of the most attractive topic in the field of microbial ecology. The relative importance of AOA and AOB in nitrogen cycle currently is still under debate since significant variations in the relative abundance, community structure and activity between them under different environmental conditions were observed. This discrepancy could be attributed to differences in the physiological ecology of AOA and AOB as evidenced by kinetics and genomes of cultures and environmental samples studies. Metabolic pathway and environmental factors like ammonia concentration, pH, dissolved oxygen and temperature were potential factors causing niche differentiation between AOA and AOB. Here, current knowledge of differences in the physiology, phylogeny, environmental responses and metabolic pathway between AOA and AOB were summarized, in order to gain deep insight into their relative contribution to nitrogen cycling under different environments. Finally, the future perspectives of AOA and AOB were proposed.