The　shift　of　nitrifier　population　within　a　partial　nitrification　reactor　was　investigated　using　fluorescence　in-situ　hybridization　(FISH)　techniques　and　the　floc　morphology　was　observed　using　scan　electron　microscope　(SEM).　Partial　nitrification　to　nitrite　was　achieved　quickly　by　using　real-time　aeration　duration　control　when　domestic　wastewater　was　treated　in　a　lab-scale　sequencing　batch　reactor　(SBR).　The　average　nitrite　accumulation　ratio　was　above　93%.　The　morphology　photographs　observed　using　SEM　indicated　that　the　sludge　showed　a　shift　towards　spherical　and　small　rod-shaped　clusters　from　the　diverse　morphology.　FISH　analysis　showed　that　ammonia-oxidizing　bacteria　(AOB)　gradually　out-competed　nitrite-oxidizing　bacteria　(NOB).　AOB　population　percentage　increased　from　3.5%　(during　the　start-up　period)　to　8.5%　(after　achieving　nitritation　for　102　days),　while　NOB　population　percentage　decreased　from　3.1%　to　less　than　0.5%.　Accordingly,　the　long-term　operation　with　the　use　of　real-time　aeration　duration　control　was　not　only　favorable　for　AOB　community　optimisation,　but　also　for　the　achievement　of　partial　nitrification　in　practice.