The　role　of　fungi　in　aerobic　granular　sludge　remains　unknown.　This　study　explored　the　formation　and　instability　of　halophilic　aerobic　granular　sludge　(HAGS)　induced　by　fungi　in　a　continuous　flow　reactor　(CFR)　figured　with　an　aeration　tank　and　a　two-zone　sedimentation　tank.　HAGS　with　a　particle　size　of　420.10　±　1.13　μm　was　successfully　cultivated　by　increased　hydraulic　shear　force　(HSF).　Increasing　HSF　stimulated　microorganisms　such　as　unclassified_f_Rhodobacteraceae,　Muricauda,　and　Raineyella　to　secrete　more　extracellular　polymeric　substances　(EPS)　with　a　high　protein　(PN)　content　(81.03　±　2.65　%).　The　peeled　filamentous　fungal　fragments　could　act　as　colonization　carriers　to　connect　microorganisms.　The　mature　HAGS　had　excellent　removal　efficiency　of　chemical　oxygen　demand　(COD;　96.20　±　1.19　%)　and　ammonia　(92.13　±　5.36　%)　from　20　g/L　saline　wastewater.　However,　HAGS　was　disintegrated　due　to　the　fast　growth　of　fungi,　mainly　unclassified_f_Nectriaceae,　resulting　in　the　deterioration　of　the　sludge　settling　performance　(SVI5　=　499.05　±　7.80　mL/g).　Filamentous　fungi　can　use　EPS　secreted　by　bacteria　under　anaerobic　and　aerobic　conditions.　The　excess　EPS　consumption　finally　destroyed　the　EPS　and　bacteria　network.　This　study　revealed　the　role　of　fungi　in　the　formation　and　instability　of　HAGS　in　CFR,　providing　the　basis　for　maintaining　long-term　HAGS　stability.　©　2024　Elsevier　Ltd