Emissions　of　methane　(CH4),　a　major　greenhouse　gas,　should　be　cut　by　at　least　30%　by　2030　according　to　the　last　Conference　of　the　Parties,　CoP26.　Aquaculture　pond　is　a　major　CH4　emitter,　yet　the　microbial　mechanisms　ruling　methanogenesis　by　degradation　of　organic　matter　in　sediments　remain　unclear.　In　particular,　the　respective　roles　of　hydrogenotrophic　and　acetoclastic　methanogenesis,　and　the　impact　of　aquaculture　farming　practices　are　unknown.　We　studied　methanogenesis　in　the　surface　sediments　from　a　freshwater　and　an　oligohaline　pond　before,　during,　and　after　shrimp　farming.　Hydrogenotrophic　and　acetoclastic　contributions　were　distinguished　by　acetoclastic　inhibition　with　methylfluoride　(CH3F),　and　by　13C-analysis　of　CO2　and　CH4.　We　also　monitored　the　methanogenic　community　structure,　dissolved　organic　carbon　(DOC)　levels,　carbon　to　nitrogen　(C/N)　ratios,　and　humification　indices　derived　from　Fourier　transform　infrared　spectroscopy.　The　results　reveal　that　aquaculture　farming　practices　increased　methanogenesis　rates,　and　these　increases　were　explained　by　higher　levels　of　DOC　and　lower　C/N　ratios　during　farming.　Of　the　total　methane　produced,　51%–78%　was　by　hydrogenotrophic　methanogenesis.　However,　the　total　methane　contribution　from　acetoclastic　methanogenesis　increased　from　approximately　22%　before　farming　to　approximately　45%　during　and　after　farming,　with　a　decreasing　isotope　fractionation　factor　αc　and　an　increasing　relative　abundance　of　Methanosaeta　acetoclastic　methanogen.　All　humification　indices　decreased　during　and　after　farming　compared　to　before　farming　due　to　the　input　of　polysaccharide-rich　aquafeed.　The　close　relationship　between　the　humification　indices　and　methanogenesis　pathways　indicates　that　the　changes　in　sediment　substrate　quality　drove　the　variation　in　the　methanogenesis　pathways.　Increases　in　salinity　decreased　the　methanogenesis　rates　but　did　not　change　the　methanogenesis　pathways.　Overall,　our　findings　reveal　that　aquaculture　farming　practices　increase　methanogenesis　rates　and　favor　acetoclastic　over　hydrogenotrophic　methanogenesis,　and　that　adjusting　shrimp　diets,　increasing　salinity,　and　removing　residual　aquafeed　could　reduce　methanogenesis.　©　2022　Elsevier　B.V.