The effect of the variation of aeration time on the microorganisms was investigated in sequencing batch reactor (SBRs). The cycling time in four SBRs was adjusted to 12 hours and then included different aerobic times as 1 hr, 2.5 hr, 4 hr and 5.5 hr, respectively. Four SBR systems have been operated and investigated for over 40 days. As the increase of aeration time, the consumption of glycogen within sludge at the 1st non-aeration time a little bit was increased and the production of glycogen at the aeration time was increased. Also, the produced PHB amounts and PHB production rate at the 1st non-aeration time were increased as the decrease of aeration time, which showed the activation of the phosphorus removal. The ratios of nitrifying microorganisms' number and GAOs to the total microorganisms' number in SBRs was decreased as the decrease of the aeration time, however, the PAOs ratio was almost constant irrespective of the variation of aeration time.