© 2016 Elsevier B.V. The Amazon Rainforest plays major roles in global carbon and nitrogen cycling. Despite this region's immense importance, deforestation and pasture creation are still occurring at alarming rates. In this study, we investigated the effects of land-use change on aerobic ammonia-oxidizers in primary rainforest, young and old pasture, and secondary forest in Rondônia, Brazil. Forest-to-pasture conversion decreased soil nitrate, phosphorus, and exchangeable acidity contents that recovered to pre-disturbance levels as pastures aged or were abandoned and formed secondary forest. The ammonia-oxidizing community, numerically dominated by thaumarchaea, shifted due to land-use change, both in terms of gene abundance and community structure. However, thaumarchaeal ammonia monooxygenase gene abundances did not correlate with any measured soil physicochemial parameters. Phylogenetic analyses showed that community structural changes in ammonia-oxidizing thaumarchaea are driven by a shift away from primary rainforest, old pasture, and secondary forest clusters to separate clusters for young pasture. Additionally, the nearly complete disappearance in young pasture, old pasture, and secondary forest sites of a thaumarchaeal genus, the Nitrosotalea, indicates that land-use change can have long lasting effects on large portions of the thaumarchaeal community. The results of this study can be used as a conceptual foundation for determining how ammonia-oxidizers become altered by land-use change in South American tropical forests.