This study was carried out to isolate and identify pathogenic microorganisms associated with deterioration of tomato fruits. Fruit samples of infected and non-infected tomatoes were collected from two open markets, Oja-Oba and Sabo in Osogbo, Nigeria. Each of the tomato was cut and the liquid content inoculated on nutrient agar and potato dextrose agar, incubated at 37 0C and 25 0C, respectively, and observed from 24 hours to 5 days, after which different colonies obtained were identified using slide culture technique. Two bacteria, Staphylococcus aureus and Bacillus spp, as well as two fungi Aspergillus flavus and Rhizopus stolonifer were observed in the tomato samples in both markets. Prevalence indices revealed that isolated pathogens is higher at Sabo market than Oja-Oba market. Pathogenicity tests also revealed that both of bacteria and fungi caused fruit decay. Consumers’ awareness on potential health hazards of consuming relatively cheaper and pathogen contaminated spoilt fruits should be intensified.