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Abstract Viable and metabolically active fungi in toxic mixed liquors, treating landfill leachates and municipal wastewaters, were identified by culture depending methods. A selective culture medium consisting of wastewater and agar (WA) restrained fungi that could be randomly present (94% of the 51 taxa retrieved on WA were sample-specific), overcoming the problem of fast growing fungi or mycoparasite fungi. Moreover, WA allowed the isolation of fungi with a possible role in the degradation of pollutants typically present in the two wastewaters. Phoma medicaginis var. medicaginis , Chaetomium globosum, and Geotrichum candidum were mainly found in municipal wastewater, whereas Pseudallescheria boydii , Scedosporium apiospermum, Aspergillus pseudodeflectus , and Scopulariopsis brevicaulis were typical of landfill leachate. Graphical abstract fx1 Highlights • Wastewater treatment may benefit from autochthonous fungal bioaugmentation. • Sludge from municipal wastewater treatment is more toxic than landfill leachate. • Wastewater-Agar is preferable for isolation of useful sample-specific fungi. • Phoma , Chaetomium , and Geotrichum could degrade molecules in municipal wastewaters. • Scedosporium , Aspergillus , Scopulariopsis could degrade molecules in leachates. [ABSTRACT FROM AUTHOR]