Tomatoes (Solanum lycopersicum Linn) are one of the most consumed fruits in Nigeria and the world at large but they are highly susceptible to microbial spoilage. Consumption of these spoilt tomatoes could increase the risk of food poisoning and also cause serious health issues which are of public health concern. This study was therefore designed to investigate the bacteria and fungi associated with spoilt tomatoes being sold in some selected markets in Ondo city. Different media (Nutrient, MacConkey, Mannitol Salt, Salmonella –Shigella, Eosin Methylene Blue, Sorbitol MacConkey and Potato Dextrose agar) were used for the determination of the total viable bacterial and fungal counts from the samples collected from Odoshida, Adeyemi and Iyalaje markets in Ondo using the pour plate technique. The isolates obtained after subculturing were characterized based on their cultural, morphological and biochemical characteristics. The total bacterial count ranged from 1.25 ×108 to 8.06 ×108cfu/mL while the total fungal count ranged from 2.75 ×105 to 5.65 ×106 cfu/mL. The identified bacteria obtained were Staphylococcus species, Proteus species, Salmonella species, Pseudomonas species, Escherichia coli, Klebsiella species, Shigella species, Enterobacter species and Bacillus species, while the fungi were Alternaria species, Penicillium species, Aspergillus species, and Rhizopus species. This study has shown that all the isolates obtained from the selected samples are of public health concerns because of their pathogenic and toxigenic nature; an indication that spoilt tomatoes ordinarily should not be consumed or consumed with utmost caution.