A bench-scale anaerobic/oxic sequencing batch reactor (SBR) was operated for 35 days with peptone and acetate fed as carbon sources during the start-up phase. In order to find quinone biomarkers representing bacteria the play important roles in priming the enhanced biological phosphorus removal (EBPR) process, the time variations of 12 quinone species and EBPR activities were quantitatively compared in the SBR. Both phosphate release rate and specific phosphate release rate increased at the beginning of the operation and reached maximum on the 21st day. It was interpreted kinetically that the concentration of phosphate-accumulating organisms (PAOs) in the reactor and the fractional percentage of PAOs in the sludge increased in the first 21 days. Only MK-10 showed a good correlation with EBPR activity through out this period, and therefore, MK-10 could be a candidate biomarker. Since Q-9 and MK-7 showed good correlations only in the first seven days, these two quinone species may be present in bacteria that play certain roles during the early phase of EBPR development.