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Isolation, identification and pathogenicity of fungal organisms causing postharvest spoilage of tomato fruits during storage was carried out. Tomato fruits showing symptoms of rot were collected from the store house. Small sizes were cut and surface sterilized in 1% of Sodium hydrochloride and rinsed in several changes of sterile distilled water. They were plated on Potato Dextrose Agar (PDA) and observed for fungal growth. Identification was done macroscopically and microscopically. For pathogenicity, healthy tomato fruits were plugged with pure cultures of the fungal isolates and disease incidence and severity were evaluated. Five fungi namely Aspergillus flavus, Penicillium waksmanii, Botryodiplodia theobromae, Fusarium oxysporum and Colletotrichum asianum were isolated. Incidence of decay on healthy tomato fruits was 100% for all fungal isolates while the control was 0%. T-test revealed significant differences between the inoculated and the controls at 1% and 5% levels of probability. Severity of decay ranged from 51–53% for all fungal isolates, while the controls showed 0%. T-test revealed significant differences between the inoculated and the control at 1% and 5% levels of probability. Pathogenic microorganisms on tomato are a potential health hazard to man and animals following ingestion.