Two enhanced biological phosphorus removal (EBPR) sequencing batch reactors (SBR1, SBR2) treating liquid dairy manure were operated with the same hydraulic retention time (HRT) and solids retention time (SRT), but with different aeration cycles. During eight months of operation, both SBRs achieved good removal of total phosphorus (P) (TP; 56.8 and 73.5% for SBR1 and SBR2 respectively) and of orthophosphate (OP; 76.2 vs. 82.7%, P < 0.05). Growth dynamics of presumptive phosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs) were examined by quantitative polymerase chain reaction (qPCR). SBR1 was enriched with a greater abundance of PAOs while SBR2 was characterized by a greater abundance of GAOs. These results demonstrate the capability of EBPR of dairy manure and challenge conventional wisdom, since greater abundance of PAOs in EBPR system was not associated with improved OP removal and greater abundance of GAOs did not indicate deterioration of the EBPR system.