The Pilot Unit of CNRS, France, developed new tools and strategies for the investigation of microbial and especially fungal secondary metabolites from isolation and structural elucidation to biosynthetic pathways. Recent achievement in the field will be illustrated through diverse examples (sporochartines, geralcins, SCH-Sch-642305 ...) highlighting the involvement of the pilot unit in national, European and international projects dedicated to the fungal metabolite valorization.