Technical Abstract: Although anaerobic lagoons are used globally for livestock waste treatment, their detailed microbial cycling of nitrogen is only beginning to become understood. Within this cycling, nitrification can be performed by organisms which produce the enzyme ammonia monooxygenase (AMO). For denitrification, the reduction of nitrite to nitric oxide can be catalyzed by two forms of nitrite reductases (Nir), and N2O-N can be reduced by nitrous oxide reductase by the gene nosZ. The objectives of this investigation were as follows: 1) quantify the abundance of the amoA, nirK, nirS, and nosZ genes; 2) evaluate the influence of environmental conditions on their abundances; and 3) evaluate their abundance relative to denitrification enzyme activity (DEA). The analyses were via Real-Time quantitative PCR (qPCR), with samples collected from eight typical, commercial anaerobic, swine wastewater lagoons located in the Carolinas. The four genes assayed in this study were present in all eight lagoons. Their abundances relative to total bacterial populations were 0.04% (amoA), 1.33% (nirS), 5.29% (nirK), and 0.27% (nosZ). When compared to lagoon chemical characteristics, both amoA and nirK correlated with several measured variables. Neither nirS nor nosZ correlated with any measured environmental variables. While no gene measured in this study correlated with actual or potential DEA, nosZ did correlate with the disparity between potential and actual DEA. As with other investigations, analyses of these genes provide useful insight while revealing the underlying greater complexity of nitrogen cycling within swine waste lagoons.