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Tomato contains large amount of water which makes it more susceptible to spoilage by fungi. These fungi that spoil tomatoes produce mycotoxins that are detrimental to human health. This study was therefore carried out to isolate, characterize and identify the fungi associated with the spoilage of tomato fruits sold in Okpuno, Amaudo, Eke-Awka, Nodu and Amaikwo Markets in Awka, Nigeria. The average fungal counts ranged between 1.3 x 10 3 and 2.0 x 10 3 cfu/ml, while the fungal isolates were Aspergillus niger, Rhizopus stolonifer, Fusarium oxysporum, Saccharomyces cerevisiae, Alternaria alternata, Penicillium digitatum and Geotrichum candidum. The percentage occurrence of the isolates in the fruits from Eke Awka was the highest (32.73%) while that of the fruits from Nodu market was the least (12.73%). Aspergillus niger had the highest percentage occurrence (47.27%) in the fruits studied, with Saccharomyces cerevisiae and Geotrichum candidum having the lowest percentage occurrence (3.64%). Pathogenicity test result showed that Aspergillus niger also had the highest decay diameter of 30mm in the healthy tomato fruits while Geotrichum candidum had the lowest decay diameter. Proper handling and adequate storage facilities must therefore be employed to prolong the shelf life of tomato fruits.

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