We analyzed denitrifying bacterial population dynamics in two wastewater treatment plants. For analyzing the population dynamics, we applied the PCR-DGGE method for targeting nirS genes, which code cytchrome cd1-type nitrite reductase. One plant treats Coke-oven wastewater (CW) and the other treats synthetic wastewater (SW) such as CW. The CW and SW mainly contained phenol, thiocyanic ion (SCN-) and thiosulfuric acid (S2O3-), and the 2 plants were configured with anoxic and aerobic tanks, respectively. Bacteria in the plants could denitrify using phenol, SCN- and S2O3- as electron acceptors. By analyzing nirS genes in the plants for a few months, we determined the partial denitrifying bacterial population in the plant and deduced bacteria that actually denitrify using phenol, SCN- and S2O3-. As far as we know, this is the first study on the analysis of the bacterial community in a CW treatment plant.