Completely　autotrophic　nitrogen　removal　over　nitrite　(CANON)　was　an　innovative　nitrogen　removal　process,　especially　for　ammonia-rich　and　low　COD　concentration　wastewater,　so　it　was　meaningful　to　investigate　the　microbial　ecology　of　nitrogen　removal　bacteria　in　CANON　system.　Polymerase　chain　reaction　(PCR),　cloning　and　real-time　PCR　(qPCR)　techniques　were　applied　to　investigate　the　abundance　and　diversity　of　AOB,　NOB,　DNB　and　anammox　bacteria　in　two　CANON　systems.　The　effect　of　different　sludge　form　on　their　abundance　was　also　studied.　qPCR　results　showed　that　the　average　abundance　of　AOB,　NOB,　DNB　and　anammox　bacteria　were　in　the　orders　of　magnitude　of　1010,　109,　108　and　1010　copies/g　dry　sludge,　respectively,　which　indicated　that　AOB　and　anammox　bacteria　were　the　most　abundant　species　and　played　major　roles　in　nitrogen　removal　in　CANON　system.　For　diversity　analysis,　DNB　was　in　greatest　diversity,　being　divided　into　five　clusters　and　attributed　to　a　total　of　more　than　ten　genera;　The　anammox　bacteria　was　of　less　diversity　and　mainly　belonged　to　Candidatus　Brocadia　cluster　and　Candidatus　Kuenenia　cluster;　AOB　was　attributed　to　N.　europaea　cluster　and　N.　eutropha　cluster　of　Nitrosomonas　group.　However,　for　NOB,　only　Nitrospira　marine　cluster　appeared.　The　sludge　form,　flocculent　activated　sludge　and　biofilm,　also　affected　their　abundance.　Flocculent　activated　sludge　was　more　suitable　for　the　growth　of　AOB,　biofilm　was　more　suitable　for　the　growth　of　DNB　and　anammox　bacteria;　However,　it　was　unclear　which　kind　of　sludge　form　was　favorable　for　the　growth　of　NOB.　This　study　provided　microbial　foundation　for　optimizing　CANON　system　to　improve　nitrogen　removal　efficiency.　©　2016,　The　Editorial　Board　of　Journal　of　Basic　Science　and　Engineering.　All　right　reserved.