The potential of a pulp and paper mill residues compost for the control of crown and root rot of greenhouse-grown tomato caused by Fusarium oxysporum f. sp. radicis-lycopersici was ultrastructurally investigated. Peat moss amended with compost substantially reduced disease-associated symptoms. Addition of Pythium oligandrum to either peat moss alone or peat moss amended with compost resulted in a considerable reduction in disease incidence compared with controls grown in peat moss alone. Histological and cytological observations of root samples from Fusarium-inoculated plants revealed that the beneficial effect of compost in reducing disease symptoms is associated with increased plant resistance to fungal colonization. One of the most prominent facets of compost-mediated induced resistance concerned the formation of physical barriers at sites of attempted fungal penetration. These structures, likely laid down to prevent pathogen ingress toward the vascular elements, included callose-enriched wall appositions and osmiophilic deposits around the sites of potential pathogen ingress. Invading hyphae, coated by the osmiophilic material, showed marked cellular disorganization. The use of the wheat germ agglutinin-ovomucoid-gold complex provided evidence that the wall-bound chitin was altered in severely damaged hyphae. A substantial increase in the extent and magnitude of the cellular changes induced by compost was observed when P. oligandrum was supplied to the potting substrate. This finding corroborates the current concept that amendment of composts with specific antagonists may be a valuable option for amplifying their beneficial properties in terms of plant disease suppression.