Mycotoxins are secondary metabolites produced by fungi that can contaminate food, both human and animal feed at all stages of the food chain. A number of factors play a role in the proliferation of mycotoxins such as climate, humidity, harvest and storage conditions. This study was looking at the occurrence and identification of the fungi obtained from the cereal grains in the central district of Botswana. Samples collected were yellow maize (18), white maize (4), millet (10), cowpeas (11), sorghum (11) and china peas (1) each weighing about 500 g. Upon the arrival of samples, water activities of the samples were obtained. Seeds were sterilized in sodium hypochlorite, to be plated onto PDA for fungal extraction. The polymerase Chain reaction was used for the identification of the fungi and samples were sent to Inqaba laboratories for sequencing. The results showed that yellow maize was contaminated by Fusarium, A. niger and A. flavus; white maize was contaminated by F. proliferatum, F. fujikuroi and Gibberella moniliformis; red sorghum was contaminated by A. flavus, A.oryzae, Penicillium, Alternaria and Chaetomium muelleri; millet was contaminated by Epicoccum sorghinum and curvularia branchyspora and cowpeas were contaminated by Aspergillus and Alternaria species. Overall the most contaminated cereal product was millet, yellow maize, white maize, cowpeas and red sorghum at 40%, 37%, 27%, 10% and 4% respectively.