Aflatoxins are secondary metabolites produced by fungi species from the genus Aspergillus, notably A. flavus, A. parasiticus and A. nomius, which develop naturally in food products and tend to cause wide array of toxic effects in several animal species, including humans. Aflatoxins are typically reported in dry food commodities such as cereals, spices, and dry fruits. This research was conducted in Ido-Osi, Efon, and Emure Local Government Areas in Ekiti State, Nigeria. Three samples; Local rice (Oryza sativa L), Maize (Zea mays) and Groundnut (Arachis hypogaea L) were obtained from three popular markets from each local government. About 10 grains of each sample were selected at random into separate petri plates and surface sterilized in 1% hypochlorite for 3 minutes. The grains were rinsed several times with distilled water. The organisms associated with the samples were isolated using Direct plating method while the aflatoxin content was determined using ELIZA. The result showed the occurrence of five (5) different fungal species distributed among the stored foods. These include: Aspergillus spp., Rhizopus spp. Penicillium spp. Mucor spp. and Botrytis spp. The species determination was confirmed by PCR with the primers specific for the ITS-rDNA region sequencing. The organisms were confirmed to the species level to be; Aspergillus flavus and Trichoderma viridie. Aflatoxin B1 was present in all the samples in which sample 6 has the highest values of 240ppb while aflatoxin B2 was relatively low. The prevalence of Aspergillus flavus in the stored foods is above 50%, which is very high and indicate the possible highlevel production of aflatoxin in food samples under study.