The　distribution　of　functional　bacteria　alone　the　bio-filter　of　a　up-flow　biological　aerated　CANON　reactor　was　investigated　using　PCR-DGGE　techniques　based　on　the　diversity　of　amoA　and　16S　rDNA　fragments　and　the　identification　and　phylogeny　were　performed　by　molecular　clone　methods.　Besides,　the　morphology　was　observed　using　scan　electron　microscope　(SEM)　in　this　study.　The　SEM　photographs　indicated　a　diverse　morphology,　of　which　spherical　and　elliptical　(0.2-1.0　μm)　were　predominant.　The　PCR-DGGE　results　indicated　a　much　better　diversity　and　bigger　population　of　ammonia　oxidizing　bacteria　under　a　depth　of　500　mm,　while　ANAMMOX　bacteria　showed　a　low　diversity　and　the　population　increased　in　some　degree　from　top　to　bottom　along　the　filter.　Phylogenetic　analysis　indicated　that　Nitrosococcus　and　Nitrosomonas　related　ammonia　oxidizing　bacteria　and　Candidatus　Kuenenia　stuttgariensis　like　ANAMMOX　bacteria　existed　in　the　reactor.　Based　on　the　species　traits　and　the　distribution　of　functional　bacteria　along　the　filter,　some　strategies　should　be　made　to　improve　the　partition　function　and　change　the　filter　material,　aiming　at　enhancing　nitrogen　removal　and　impact　resistance　of　the　reactor.