AbstractBACKGROUNDSeed germination is a key phase of the parasitic plant life cycle that is stimulated by the secondary metabolites, mainly strigolactones (SLs), secreted by the host roots. Interventions during this stage would be particularly suitable for parasitic weed management practices, as blocking these chemical signals would prevent seed germination and thus parasite attack. Four fungal strains with different ecological functions were considered for their possible ability to metabolise SLs: Fusarium oxysporum and F. solani, biocontrol agents of Phelipanche ramosa; Trichoderma harzianum, a potential biopesticide; Botrytis cinerea, a phytopathogenic fungus. Four different SLs [the natural strigol, 5‐deoxystrigol (5DS) and 4‐deoxyorobanchol (4DO), and the synthetic analogue GR24] were added to fungal cultures, followed by determination of the SL content by liquid chromatography–tandem mass spectrometry.RESULTSDifferences were observed among microorganisms, treatments and SLs used. T. harzianum and F. oxysporum were the most capable of reducing the SL content; considering the whole set of fungi used, 5DS and 4DO proved to be the most degradable SLs.CONCLUSIONSBeneficial microscopic fungi could differently be used for biocontrolling parasitic weeds, acting as a ‘physiological’ barrier, by preventing the germination of their seeds through the ability to biotransform the stimulatory signals. © 2016 Society of Chemical Industry