Ammonia　oxidation　is　the　first　and　rate-limiting　step　of　nitrification,　which　was　thought　to　be　only　performed　by　ammonia-oxidizing　bacteria　(AOB).　In　recent　years,　ammonia-oxidizing　archaea　(AOA)　was　also　confirmed　to　take　part　in　ammonia　oxidation.　The　diversity　and　abundance　of　AOA　have　been　investigated　in　various　environments,　however,　little　is　known　regarding　the　AOA　in　the　completely　autotrophic　nitrogen　removal　over　nitrite　(CANON)　wastewater　treatment　process.　In　this　study,　the　abundance　and　diversity　of　AOA　were　investigated　in　the　biofilm　and　flocculent　activated　sludge　collected　in　a　lab-scale　(L)　CANON　system　and　a　pilot-scale　(P)　CANON　systems,　respectively.　The　quantitative　real　time　PCR　(qPCR)　was　applied　to　investigate　the　abundance　of　AOA　and　the　diversity　of　AOA　was　determined　by　polymerase　chain　reaction　(PCR),　cloning　and　sequencing.　The　qPCR　results　showed　that　the　average　abundance　of　AOA　amoA　gene　of　L　and　P　was　2.42×106　copies·　g-1　dry　sludge　and　6.51×106　copies·g-1　dry　sludge,　respectively.　The　abundance　of　AOA　in　biofilm　was　10.1-14.1　times　higher　than　that　in　flocculent　activated　sludge.　For　P　system,　the　abundance　of　AOA　in　flocculent　activated　sludge　was　1.8　times　higher　than　that　in　biofilm.　The　results　indicated　that　the　abundance　of　AOA　might　be　affected　by　different　sludge　morphology.　The　diversity　of　AOA　in　P　system　was　extremely　limited,　only　one　OTU　was　observed,　which　was　classified　into　Nitrosopumilus　subcluster　5.2.　The　diversity　of　AOA　in　L　system　was　higher,　eight　OTUs　were　observed,　which　were　classified　into　five　genera:　Nitrososphaera　subcluster　9,　subcluster　8.1,　subcluster　4.1,　subcluster　1.1　and　Nitrosopumilus　subcluster　5.2.　The　diversity　and　abundance　of　AOA　were　different　in　CANON　systems　with　different　sludge　morphology.　AOA　may　play　an　important　role　in　ammonia　oxidation　in　CANON　system.　©,　2015,　Huanjing　Kexue/Environmental　Science.　All　right　reserved.