A　modified　University　of　Cape　Town　(MUCT)　process　was　used　to　treat　real　municipal　wastewater　with　low　carbon　to　nitrogen　ratio　(C/N).　To　our　knowledge,　this　is　the　first　study　where　the　influence　of　nitrite　accumulation　on　＂Candidatus　Accumulibacter＂　clade-level　population　structure　was　investigated　during　nitritation　establishment　and　destruction.　Real　time　quantitative　PCR　assays　were　conducted　using　the　polyphosphate　kinase　1　gene　(ppk1)　as　a　genetic　marker.　Abundances　of　total　＂Candidatus　Accumulibacter＂,　the　relative　distributions　and　population　structure　of　the　five　＂Candidatus　Accumulibacter＂　clades　were　characterized.　Under　complete　nitrification,　clade　I　using　nitrate　as　electron　acceptor　was　below　5%　of　total　＂Candidatus　Accumulibacter＂.　When　the　reactor　was　transformed　into　nitritation,　clade　I　gradually　disappeared.　Clade　IID　using　nitrite　as　electron　acceptor　for　denitrifying　phosphorus　(P)　removal　was　always　the　dominant　＂Candidatus　Accumulibacter＂　throughout　the　operational　period.　This　clade　was　above　90%　on　average　in　total　＂Candidatus　Accumulibacter＂,　even　up　to　nearly　100%,　which　was　associated　with　good　performance　of　denitrifying　P　removal　via　nitrite　pathway.　The　nitrite　concentrations　affected　the　abundance　of　clade　IID.　The　P　removal　was　mainly　completed　by　anoxic　P　uptake　of　about　88%.　The　P　removal　efficiency　clearly　had　a　positive　correlation　with　the　nitrite　accumulation　ratio.　Under　nitritation,　the　P　removal　efficiency　was　30%　higher　than　that　under　complete　nitrification,　suggesting　that　nitrite　was　appropriate　as　electron　acceptor　for　denitrifying　P　removal　when　treating　carbon-limited　wastewater.　(C)　2015　The　Authors.　Published　by　Elsevier　Ltd.