Recent progress in ammonia-oxidizing archaea (AOA) studies suggested their significant contributions to the global nitrogen cycling by possessing the capacity to oxidize ammonia to nitrite, and phylogenetic analysis categorized AOA into a novel archaeal phylum, the Thaumarchaeota lineage. AOA have widespread occurrence in terrestrial ecosystems, unique mechanisms for nitrification, better adaptation to low-pH pressures, and strikingly lower ammonia requirement compared with ammonia-oxidizing bacteria (AOB). Previous perceptions that, microbial ammonia oxidation in acidic soils was minimal, and entirely meditated by autotrophic bacteria and occasionally by heterotrophic nitrifiers, have been challenged. Relative contributions of autotrophic AOA and AOB to ammonia oxidation were reported to controversially vary in different soils, but ammonia availability, which was largely restricted under acidic conditions, seemed to be the key driver. Acidic soils are particularly characterized by high amount of hydrogen ions in soil solutions which could shift the equilibrium from ammonia to ammonium, by this way producing a relatively ammonia-limited environment. Theoretically predicted ammonia concentrations in acidic soils were below the substrate threshold of AOB and remarkably high ammonia affinity of AOA raised the supposition that thaumarchaea could represent the dominant ammonia-oxidizing group in acidic environments with low ammonia availability. Recently, the functional dominance of thaumarchaea over its bacterial counterpart and autotrophic thaumarchaeal ammonia oxidation activity in acidic soils has been compellingly confirmed by DNA-stable isotope probing (SIP) experiments and the cultivation of an obligate acidophilic thaumarchaeaon, Nitrosotalea devanaterra. In this presentation, I will review the currently available knowledge concerning the history and progress of the ammonia-oxidizing microorganisms (AOB and AOA) and the mechanisms in nutrient-depleted acidic soils, comprehensively present the possible mechanisms shaping the niche differentiation of AOA and AOB, and thus strengthen the assumption that AOA dominate over AOB in the ammonia oxidation of acidic soils. The unveiling of this key process in widely-distributed acid soils would help to identify effective biological strategies for better management of terrestrial nitrogen turnover and balance in acidic soils.