Technical Abstract: The microbial mineralization of urea and uric acid results in the production of ammonia, which can lead to decreased poultry performance, malodorous emissions, and loss of poultry litter value as a fertilizer. Despite the fact that this is a microbial process, little is known about how the microbial population and in particular how ammonia-producing (ureolytic) organisms respond in poultry litter and to litter amendments such as alum (Al2(SO4)3•14H2O). The goals of this study were to monitor the temporal change in total bacterial and fungal populations and urease-producing microorganisms present in untreated litter or litter treated with 10% alum. Quantitative, real-time PCR (QRT-PCR) was used to target the bacterial 16S rDNA gene, the fungal 18S rDNA gene or the urease gene of bacterial and fungal ammonia producers in a poultry litter incubation study. In untreated poultry litter, there was a dense total (2.8 ± 0.8 X 1010 cells g-1 litter) and ureolytic (2.8 ± 1.3 X 108 cells g-1 litter) bacterial flora. When treated with alum, the bacterial population was reduced by 50% and bacterial urease producers were reduced by 90% within four weeks. In contrast, the fungal population was three orders of magnitude higher in alum-treated poultry litter than in untreated litter (3.5 ± 0.8 X 107 cells g-1 litter and 5.5 ± 2.5 X 104 cells g-1 litter by week 16, respectively). The shift in pH inhibits bacterial populations but selects for fungal organisms that may be responsible for the mineralization of organic nitrogen in alum-treated litters.