Tomato contains large amount of water which makes them more susceptible to spoilage by the action of various microorganisms. This makes the storage of this vegetable difficult. The objective of this study is to determine microbial load of tomatoes including microbial species it constitute under storage with particular reference to low temperature storage. Pour plate techniques were used to enumerate microbial load of the samples. Discrete isolated colonies from these sources were sub-cultured using streak plate method to get purified cultures for the study. Standard microbiological methods (morphologically, microscopically and biochemical tests) were subsequently used to identify the tomatoes microflora. Microorganisms generally encountered include seven bacterial species such as, Acidovorax facilis, Aminobacter aminovorans, Acidiphilium facilis, Burkholderia cepacia, Azomonas sp., Xanthobacter flavus and Azomonas insignis. Similarly, three fungal species were encountered during the study. These include Alternaria alternata lycopersi, Alternaria tenuissima and Phycomyces microspores. The investigation revealed that up to 90% of the samples were infected with one or more fungal and bacterial species. The most predominant pathogenic microbes isolated from the samples were, A. alternata lycopersi (42.0%), A. tenuissima and X. flavus (35.0%), others include A. insignis (32%), A. facilis (25%) and B. cepacia (20%). Proper handling from the farm as well as during storage and the avoidance of mixing of diseased ones with the healthy ones were identified as important factors in preventing loss.