To　investigate　the　effects　of　real-time　control　on　the　structure　of　nitrifying　communities　of　the　short-cut　nitrogen　removal　in　SBR　pilot-scale　plant　with　a　working　volume　of　54　m,　molecular　techniques　of　Fish,　PCR-DGGE　and　PCR-Cloning-Sequencing　were　used　to　analyze　ammonia-oxidizing　bacteria　(AOB)　and　nitrite-oxidizing　bacteria　(NOB)　with　the　performance　of　short-cut　nitrogen　removal.　Fish　results　show　that　in　short-cut　nitrogen　removal　process,　AOB　became　dominant　with　compared　to　NOB　and　accounted　for　3%-12%　of　the　total　biomass.　More　importantly,　no　NOB　was　detected.　PCR-DGGE　gel　results　show　that　AOB　were　phylogenetically　related　to　Nitrosomonas-like　species　with　a　melting　point　at　the　range　between　30%　to　50%.　PCR-Cloning-Sequencing　results　show　that　all　clones　were　affiliated　with　Nitrosomonas　corresponding　to　DGGE　results　and　60%　of　the　clones　were　affiliated　with　Nitrosomonas　europaea.