Infiltration ofPenicillum janczewskiiconidia or its culture filtrate into melon and cotton leaves induced systemic resistance and protected the lower part of the stem of melon and cotton plants againstRhizoctonia solani, leading to up to a 100% reduction in the incidence of damping-off. Hypersensitive reaction like responses were observed in melon and tobacco, but not in cotton. Peroxidase activity, associated with induced systemic resistance, increased in treated plants of both species compared to the control plants. Gel electrophoresis of peroxidases from melon plants treated with culture filtrate exhibited enhanced activity of all three isozymes present in untreated plants, but mostly of the slowest migrating isozyme. Phenylalanine ammonia-lyase activity in stems of melon plants treated withP. janczewskiior its culture filtrate increased two-fold compared to the untreated plants. Western blot analyses revealed induction of β-1,3-glucanase, a pathogenesis-related protein, and hsp70, a member of the heat shock protein family in melon. Altered root development was observed in cotton plants infiltrated withP. janczewskiiconidia or its metabolites. Our results suggest that treating leaves withP. janczewskiior its culture filtrate triggers the signal transduction cascade, activating different defence genes in melon and cotton, thus protecting the lower parts of the stem.