Soils may be the most important habitats for micro-organisms that produce atmospheric trace gases such as methane (CH₄), nitrous oxide (N₂O) and nitric oxide (NO). One of the principal reasons for the alteration of the fluxes of these gases to the atmosphere, especially in the tropics, may be deforestation or land disturbance for human activities such as the creation of croplands or pastures. The purpose of this study was (1) to determine if land use history has an effect on the densities and activities of ammonium oxidizing bacteria and densities of denitrifying bacteria and (2) to determine if different genera of ammonium bacteria are present in the soils of the study sites in the different life zones of Puerto Rico. Concentrations of nitrifying bacteria ranged from 5.5 × 10² to 2.3 × 10⁵ MPN/g soil whereas concentrations of denitrifying bacteria ranged from 2.2 × 10⁵ to 1.5 × 10⁶ MPN/g of soil. Statistical analyses showed no significant difference between the densities of these bacteria in soils and the type of land use but there was a significant difference between the densities of bacterial populations and the months of sampling in one of the areas that was studied. The nitrification potential rates (measures activities of ammonium oxidizing bacteria) were not statistically significant between the soil soils studied in the same area or between the months in which these were studied. It seems that the land use does not affect the concentrations of these bacterial populations as much as the variations that occur seasonally (monthly). Ammonium oxidizing bacteria of the genus Nitrosospira are more abundant, than the genus Nitrosomonas in the soils studied.