A　lab-scale　partial　nitrifying　sequencing　batch　biofilm　reactor　was　a　successful　start-up.　Denaturing　gradient　gel　electrophoresis　(DGGE)　was　used　to　investigate　the　bacterial　community　dynamics　in　three　periods　together　with　inocula　sludge　at　ambient　temperature.　The　DGGE　profiles　of　bacteria　and　Shannon-Wiener　index　(H＇)　results　showed　that　high　free　ammonia　(FA)　concentration　referred　to　lower　diversity　in　the　bioreactor　system.　Cluster　analysis　indicated　that　microorganism　in　period　III　was　similar　with　inocula　sludge　and　was　different　from　that　in　periods　I　and　II.　Similar　results　also　appeared　in　ammonia-oxidizing　bacteria　(AOB)　community　structure　and　nitrite-oxidizing　bacteria　(NOB)　community　structure,　and　at　least　four　AOB　species　and　two　NOB　species　were　present　in　period　III,　respectively.　Phylogenetic　analysis　of　amoA　gene　sequences　showed　that　Nitrosomonas　eutropha　cluster　was　predominant　in　all　the　three　periods.　With　lower　ammonium　loads,　three　new　operational　taxonomic　units　formed　and　consisted　Nitrosomonas　sp.　Cluster.　This　article　demonstrated　that　microbial　community,　AOB,　and　NOB　diversity　were　related　with　FA　concentration　closely　at　ambient　temperature.