The dynamics of nitrogen compounds and RNA-based functional genes were characterized in the nitrification-denitrification coupling process. For the removal of residual ammonium, intermittent aeration was introduced in the denitrification reactor. N₂O production was not observed in both reactors. In both reactors, the nitrifying genes (achaeal-amoA, bacterial-amoA and hor) and denitrifying genes (narG, nirK, norB and nosZ) had a copy number of 3.92 × 10² -7.25 × 10⁵ and 2.85 × 10² -3.06 × 10⁴ per ng of DNA, respectively. These results suggest that denitrification and nitrification reactions occur in both the nitrification and denitrification reactors, respectively. Therefore, the coupling process is a promising one for the conversion of ammonium to nitrogen without generating N₂O.