Structural　disintegration　caused　by　the　overgrowth　of　filamentous　microorganisms　is　a　major　threat　to　the　stable　operation　of　aerobic　granular　sludge　(AGS).　In　this　study,　the　overgrowth　of　filamentous　fungi　was　observed　for　the　first　time　in　halophilic　aerobic　granular　sludge　(HAGS)　following　reactivation　after　250　days　of　refrigeration　storage.　The　dominant　filamentous　fungi　genera,　with　a　relative　abundance　of　98.3　+/-　0.2　%,　were　affiliated　to　the　family　Nectriaceae　(unclassified_f_Nectriaceae).　Originally　existing　in　the　HAGS　nuclei,　these　filamentous　fungi　extended　their　hypha　from　the　core　to　the　surface　of　the　HAGS　during　reactivation　in　the　wastewater　treatment　system.　The　filamentous　fungi　could　degrade　extracellular　polymeric　substances　produced　by　bacteria,　as　well　as　the　organic　matter　in　saline　wastewater,　under　both　anaerobic　and　aerobic　conditions.　These　characteristics　help　the　fungi　maintain　the　growth　advantage　when　bacteria　in　the　HAGS　were　inhibited　under　the　low　temperature　and　anaerobic　conditions.　Under　the　aerobic　condition,　fungal　growth　was　further　promoted　due　to　their　broad　carbon　utilization　and　facultative　respiration　capacities,　exerting　a　strong　competitive　advantage　against　halophilic　bacteria,　such　as　Marinobacterium,　Halomonas　and　Vibrio.　This　study　is　the　first　to　find　and　reveal　the　overgrowth　of　filamentous　fungi　in　HAGS,　providing　a　basis　to　regulate　fungal　growth　and　maintain　the　structural　stability　of　HAGS.