Laboratory scale experiments were conducted to study the deterioration of enhanced biological phosphorus removal (EBPR) due to influent ammonium concentration, and to compare the performance of two types of sequencing batch reactor (SBR) systems, a conventional SBR and sequencing batch biofilm reactor (SBBR). Both in SBR and SBBR, the total nitrogen removal efficiency decreased from 100% to 53% and from 87.5% to 54.4%, respectively, with the increase of influent ammonium concentration from 20 mg/l to 80 mg/l. When the influent ammonium concentration was as low as 20 mg/l (C : N : P=200 : 20 : 15), denitrifying glycogen-accumulating organisms (DGAOs) were successfully grown and activated by using glucose as a sole carbon source in a lab-scale anaerobic-oxic-anoxic (A2O) SBR. In the SBR, due to the effect of incomplete denitrification and pH drop, the nitrogen and phosphorus removal efficiency decreased from 77% to 33.3% when the influent ammonium concentration increased from 20 mg/l to 80 mg/l. However, in the SBBR, simultaneous nitrification/denitrification (SND) occurred, and the nitrification rate in the aerobic phase did not change remarkably in spite of the increase in influent ammonium concentration. Phosphorus removal was not affected by the increase of influent ammonium concentration.