Ammonia-oxidizing bacteria (AOB) perform the rate-limiting step of nitrification, a key ecosystem process that in part determines the fate of nitrogen in ecosystems. However, little is known about the factors that determine soil AOB diversity or composition, especially in tropical systems. Using a set of study systems in Costa Rica, we examined whether plant diversity or land-use influenced AOB diversity or composition and whether AOB diversity or composition were associated with nitrification rates. We characterized the molecular diversity and composition of AOB via polymerase chain reaction amplification, cloning, and sequencing of 16S rDNA. We found that AOB diversity or composition did not change significantly across plant diversity treatments. In contrast, AOB differed among land-use types in some measures of diversity and in composition, and differences in AOB composition among land-use types were correlated with potential rates of nitrification. Our results suggest that anthropogenic changes of ecosystems can alter microbial communities in ways that may affect the processes they mediate.