Acid soils, extensively used for nitrogen-fertilized agriculture and agroforestry, have important roles in maintaining global biogeochemical cycling and ecosystem functions. Huge inputs of nitrogen-based fertilizers into terrestrial ecosystems accelerate soil acidification, concomitantly altering the nitrogen transformation processes. Nitrification, as a critical component of the nitrogen cycle, is a microbially mediated process from ammonia to nitrate via nitrite, contributing to enormous losses of fertilizers through atmospheric emissions of greenhouse gas N2O and nitrate leaching to groundwater. However, the functionally dominant nitrifiers and underlying mechanisms for the acid soil nitrification are a long-standing mystery, which have confused scientists for more than 100 years. This century-long paradox originated from the early observations of active nitrification activity in acid soils, intensified by the failure of ammonia-oxidizing bacteria (AOB) cultures to sustain the nitrification in liquid batch under acid conditions, might be resolved by the recent progress in metagenomic, isotopic probing studies, and isolation of acidophilic ammonia-oxidizing archaea (AOA). Emerging evidence led to the supposition of the predominant role of AOA in controlling the autotrophic ammonia oxidation of acid soils, which has radically revised the previous perception that this oxidative reaction was exclusively regulated by autotrophic AOB and occasionally by heterotrophic nitrifiers. In this chapter, we review the recent progress in our understanding of the pH-impacted distribution of ammonia oxidizers, the niche differentiation of AOA and AOB shaped by acid stress, and the possible mechanisms of autotrophic nitrification in acid 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.