There　is　great　potential　to　understand　the　functional　diversity　of　microorganisms　that　are　involved　in　waste　water　treatment　through　metagenomic　analyses.　This　study　presents　the　first　metagenomic　comparison　of　taxonomic　and　functional　profiles　of　the　microbial　communities　occurring　in　different　aggregates　from　anaerobic　ammonium-oxidizing　(anammox)　bioreactors.　The　anammox　bacterial　communities　in　both　biofilm　and　granule　sludge　samples　showed　relatively　high　abundance　and　diversity　compared　with　floccular　sludge.　Four　of　the　five　known　genera　of　anammox　bacteria　were　detected　in　the　three　cultures　except　Candidatus　Jettenia,　which　was　absent　in　the　granules.　Candidatus　Kuenenia　comprised　the　major　population　of　anammox　bacteria　in　these　three　sludges,　independent　of　their　growth　morphologies.　The　genome　assembled　for　the　Candidatus　Kuenenia　in　the　granule　was　very　similar　to　the　published　reference　genome　of　Candidatus　K.　stuttgartiensis.　Genes　involved　in　the　metabolism　of　the　anammox　process　were　highly　detected　in　the　biofilm　and　granule　sludges.　In　particular,　the　abundance　of　hydrazine　synthase　gene　(hzs)　in　the　biofilm　was　around　486　times　more　pronounced　than　that　in　the　granules.　The　knowledge　gained　in　this　study　highlights　an　important　role　of　sludge　aggregate　in　affecting　community　structure　and　metabolic　potential　of　anammox　systems.