＂Candidatus　Accumulibacter＂　is　the　dominant　polyphosphate-accumulating　organism　(PAO)　in　denitrifying　phosphorus　removal　(DPR)　systems.　In　order　to　investigate　the　community　structure　and　Glade　morphotypes　of　＂Candidatus　Accumulibacter＂　in　DPR　systems　through　flow　cytometry　(FCM),　denitrifying　phosphorus　removal　of　almost　100%　using　nitrite　and　nitrate　as　the　electron　acceptor　was　achieved　in　sequencing　batch　reactors　(SBRs).　An　optimal　method　of　flow　cytometry　combined　with　fluorescence　in　situ　hybridization　and　SYBR　green　I　staining　(FISH-staining-flow　cytometry)　was　developed　to　quantify　PAOs　in　DPR　systems.　By　setting　the　width　value　of　FCM,　bacterial　cells　in　a　sludge　sample　were　divided　into　three　groups　in　different　morphotypes,　namely,　coccus,　coccobacillus,　and　bacillus.　Average　percentages　that　the　three　different　PAO　populations　accounted　for　among　total　bacteria　from　SBR1　(SBR2)　were　42%　(45%),　14%　(13%),　and　4%　(2%).　FCM　showed　that　the　ratios　of　PAOs　to　total　bacteria　in　the　two　reactors　were　61%　and　59%,　and　the　quantitative　PCR　(qPCR)　results　indicated　that　IIC　was　the　dominant　＂Candidatus　Accumulibacter＂　Glade　in　both　denitrifying　phosphorus　removal　systems,　reaching　50%　of　the　total　＂Candidatus　Accumulibacter＂　bacteria.　The　subdominant　Glade　in　the　reactor　with　nitrite　as　the　electron　acceptor　was　IID,　accounting　for　31%　of　the　total　＂Candidatus　Accumulibacter＂　bacteria.　The　FCM　and　qPCR　results　suggested　that　clades　IIC　and　IID　were　both　coccus,　Glade　IIF　was　coccobacillus,　and　Glade　IA　was　bacillus.　FISH　analysis　also　indicated　that　PAOs　were　major　cocci　in　the　systems.　An　equivalence　test　of　FCM-based　quantification　confirmed　the　accuracy　of　FISH-staining-flow　cytometry,　which　can　meet　the　quantitative　requirements　for　PAOs　in　complex　activated　sludge　samples.　IMPORTANCE　As　one　group　of　the　most　important　functional　phosphorus　removal　organisms,　＂Candidatus　Accumulibacter,＂　affiliated　with　the　Rhodocyclus　group　of　the　Betaproteobacteria,　is　a　widely　recognized　and　studied　PAO　in　the　field　of　biological　wastewater　treatment.　The　morphotypes　and　population　structure　of　Glade-level　＂Candidatus　Accumulibacter＂　were　studied　through　novel　FISH-staining-flow　cytometry,　which　involved　denitrifying　phosphorus　removal　(DPR)　achieving　carbon　and　energy　savings　and　simultaneous　removal　of　N　and　P,　thus　inferring　the　different　denitrifying　phosphorus　removal　abilities　of　these　clades.　Additionally,　based　on　this　method,　in　situ　quantification　for　specific　polyphosphate-accumulating　organisms　(PAOs)　enables　a　more　efficient　process　and　more　accurate　result.　The　establishment　of　FISH-staining-flow　cytometry　makes　cell　sorting　of　Glade-level　noncultivated　organisms　available.