Hexadecyl　trimethyl　ammonium　chloride　(ATMAC-C16)　is　a　kind　of　quaternary　ammonium　compound　(QACs)　which　is　extensively　consumed　as　disinfectants,　antimicrobials　and　surfactants.　Here,　the　partial　nitrification/　anammox　(PN/A)　system　was　exposed　to　different　levels　of　ATMAC-C16　(0-10　mg/L)　and　the　main　objective　was　to　reveal　the　long-term　microbiological　responses　of　PN/A　system　to　ATMAC-C16,　importantly,　explore　the　tolerance　of　PN/A　to　ATMAC-C16　and　the　key　resistant　strain.　Nitrogen　removal　efficiency　was　influenced　by　environmental　and　extreme　levels　of　ATMAC-C16　through　mainly　affecting　the　anammox　(hzsB)　gene.　Two　types　of　anammox,　Candidatus　Jettenia　and　Candidatus　Kuenenia,　were　enriched　under　the　pressure　of　ATMAC-C16,　which　allowed　PN/A　system　to　maintain　good　nitrogen　removal　performance.　ATMAC-C16　might　cause　the　hormesis　of　entire　microbial　population　in　PN/A　system,　leading　to　the　enhancement　of　cell　viability.　ATMACC16　decreased　the　relative　abundances　of　most　antibiotics　resistance　genes　(ARGs)　but　significantly　enriched　QACs　resistance　genes　(QRGs).　The　tolerance　of　PN/A　system　to　ATMAC-C16　might　be　strengthened　by　inducing　the　efflux　pumps　encoding　genes　(qacH-01/02).　Microbial　hosts　dynamic　and　co-selection　mechanism　among　ARGs　and　QRGs　resulted　in　the　opposite　trends　of　qacEdeltal-01/02　and　qacH-01/02.　Pseudoxanthomonas　mexicana　was　identified　as　the　ATMAC-C16　resistant　strain,　and　its　resistance　to　10　mg/L　ATMAC-C16　might　not　only　obtain　by　capturing　the　qacH　gene,　but　also　benefit　from　its　own　efflux　pump　system.　Therefore,　from　the　perspective　of　the　transmission　of　resistance　genes,　especially　for　QRGs,　the　spread　risk　of　QRGs　and　ATMAC-C16　resistant　strain　in　PN/A　technique　should　be　taken　seriously.