Aggregation　of　anammox　bacteria　is　essential　to　maintain　high　biomass　concentrations　and　prevent　the　loss　of　biomass　in　anammox　processes.　PICRUSt　(Phylogenetic　Investigation　of　Communities　by　Reconstruction　of　Unobserved　States)　was　used　in　this　study　to　predict　the　metagenomic　potentials　and　characterize　the　microbial　community　structure　and　functional　features　in　anammox　aggregates　(e.g.,　sludge　flocs,　biofilms,　and　granules).　The　results　showed　that　Candidatus　Brocadia　was　the　most　dominant　anammox　genera　in　all　aggregates　(38.0%　in　flocs,　69.4%　in　biofilm,　and　52.0%　in　granules)　and　the　functional　gene　involved　in　the　anammox　process　was　detected　in　the　highest　amount　in　biofilms,　followed　by　granules　and　flocs.　Furthermore,　the　anammox　microbial　aggregation　pathway　was　explored　that　anammox　bacteria　have　strong　motility　and　high　capability　for　early　attachment.　Anammox　bacteria　could　produce　large　amounts　of　EPS　(extracellular　polymeric　substances)　regulated　by　quinolone　and　transport　to　extracellular　environment　through　type　II　secretion　system.　The　strong　ability　of　c-di-GMP　(bis-(3　＇-5　＇)-cyclic　dimeric　guanosine　monophosphate)　synthesis　enabled　a　stable　architectural　structure　of　aggregation.　This　study　elucidated　the　aggregation　mechanism　of　anammox　microorganisms　at　the　genetic　level　to　enhance　the　stability　of　anammox　processes.　Practitioner　points　Candidatus　Brocadia　was　the　most　dominant　anammox　genera　in　aggregates.　Anammox　bacteria　have　strong　motility　and　high　attachment　capability.　Anammox　bacteria　possess　strong　EPS　synthesis　regulated　by　quinolone.　c-di-GMP　synthesis　enables　a　stable　structure　of　aggregation.