The effect of electron acceptors on denitrifying phosphorus (P) removal and its community structures in A(2)O process treating domestic wastewater was investigated using DNA based stable-isotope probing (DNA-SIP). Stable denitrifying P removal in anoxic zone of A(2)O process was achieved with an average denitrifying P removal efficiency of 72%. Results of quantitative polymerase chain reaction indicated that clade IIF was the dominant clade for denitrifying P removal. NirS, NirK and NarG were the major functional genes for denitrification. Batch tests were conducted with unlabelled and C-13-labelled sodium acetate as carbon sources, which confirmed that oxygen, nitrate and nitrite can be used as electron acceptor. High throughput sequencing for C-13-DNA samples indicated that polyphosphate accumulating organisms (PAOs) were mainly affiliated with phylum Proteobacteria. Candidatus_Accumulibacter was the major genus using oxygen and nitrate as electron acceptors. Acinetobacter was the most dominant genus using nitrate and nitrite as electron acceptors. Unclassified_f_Rhodocyclaceae appeared in three P removal systems. In the EBPR process, not only anaerobic P-release and aerobic P-uptake, but also denitrifying P removal should be considered. Different types of PAOs corresponding to different electron acceptors interacted to ensure the stable performance of nitrogen and phosphorus removal.