In　completely　autotrophic　nitrogen　removal　over　nitrite　(CANON)　process,　the　bioactivity　of　nitrite-oxidizing　bacteria　(NOB)　should　be　effectively　inhibited.　In　this　study,　the　stability　of　four　high-rate　CANON　reactors　and　the　effect　of　free　ammonia　(FA)　and　organic　material　on　NOB　community　structure　were　investigated　using　DGGE.　Results　suggested　that　with　the　increasing　of　FA,　the　ratio　of　total　nitrogen　removal　to　nitrate　production　went　up　gradually,　while　the　biodiversity　of　Nitrobacter-like　NOB　and　Nitrospira-like　NOB　both　decreased.　When　the　CANON　reactor　was　transformed　to　simultaneous　partial　nitrification,　anammox　and　denitrification　(SNAD)　reactor　by　introducing　organic　material,　the　denitrifiers　and　aerobic　heterotrophic　bacteria　would　compete　nitrite　or　oxygen　with　NOB,　which　then　led　to　the　biodiversity　decreasing　of　both　Nitrobacter-like　NOB　and　Nitrospira-like　NOB.　The　distribution　of　Nitrobacter-like　NOB　and　Nitrospira-like　NOB　were　evaluated,　and　finally　effective　strategies　for　suppressing　NOB　in　CANON　reactors　were　proposed.　(C)　2014　Elsevier　Ltd.　All　rights　reserved.