Although　efficient　removal　of　carbon　(C),　nitrogen　(N)　and　phosphorous　(P)　from　wastewater　with　low　C/N　ratio　was　achieved　in　anaerobic/aerobic　simultaneous　nitrification-endogenous　denitrification　and　phosphorus　removal　(SNEDPR)　systems,　the　removal　pathways　and　metabolic　transformations　in　this　complex　system　are　unclear.　This　work　targeted　at　developing　the　stoichiometric　models　for　denitrifying　glycogen　organisms　(DGAOs)　via　nitrite　and　nitrate　(DGAO(Ni)　and　DGAO(Na)),　and　demonstrating　a　novel　methodology　to　quantify　diverse　functional　microorganisms　(e.g.　ammonia　and　nitrite　oxidizing　bacteria,　aerobic　phosphorus　accumulating　organisms　(APAOs),　denitrifying　PAOs　(DPAOs)　and　aerobic　GAOs　(AGAOs))　for　the　removal　of　C,　N　and　P.　The　results　showed　that　the　anaerobic　intracellular　carbon　storage　(CODintra)　was　mainly　accomplished　by　GAOs,　and　PAOs　were　only　responsible　for　about　40%　of　CODintra　through　a　stable　P　release.　At　the　aerobic　stage,　84.9%　of　P　was　removed　by　APAOs　with　15.1%　left　by　DPAOs,　while　64.6%　of　N　was　removed　by　DGAOs　(45.8%　by　DGAO(Ni)　and　18.8%　by　DGAO(Na))　with　18.1%　by　DPAOs　and　173%　by　bacterial　growth.　High　proportion　of　N　removal　via　nitrite　(partial　nitrification　endogenous　denitrification)　(71%)　saved　7.3%　aeration　and　38%　intracellular　carbon　demand.　However,　AGAOs　still　activated　well　at　the　aerobic　intercellular　carbon　consumption,　which　limited　the　further　improvement　of　N　removal　efficiency.　By　elucidating　the　nutrient　removal　pathways　among　diverse　functional　microorganisms,　the　methodology　developed　in　this　study　could　accelerate　the　nutrient　removal　in　the　SNEDPR　process.　(C)　2016　Elsevier　Ltd.　All　rights　reserved.