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Increased incidence of food-borne illnesses, particularly diarrhea, have been linked in Nigeria to eating meals made with flour that have been contaminated by microbes. Our local marketplaces carry exposed and packaged cassava and plantain flour. In this investigation, bacterial and fungal isolates from the flour samples were isolated and identified using established microbiological techniques. The process used to make cassava flour differs based on the region. Freshly picked cassava roots are used to make cassava flour in West Africa, particularly in Nigeria. The roots are cleaned, chipped, and peeled. Sun-dried cassava chips are ground into a fine powder and packaged in materials that are moisture resistant. Cassava and Plantain flour are locally used in the preparation of a wide range of food I the south western part of Nigeria. However, these are sold in open air markets, with very little or no attention given to hygienic practices and are seldomly subjected to safety checks by the appropriate food safety authorities. The highest fungal count was found in Plantain flour sample pnb1 with 34 x 104 cfu/g, while the lowest count observed in both cnb6 and pnb4 with fungal counts of 1 cfu/g. Saccharomyces and Fusarium spp were the most prevalent fungi in both Plantain and Cassava flour samples. While Rhizopus oryzae was the most prevalent in the plantain flour sample and Aspergillus niger as the most prevalent in the Cassava flour with Aspergillus fumigatus and Mucor spp and Rhizopus spp as the least prevalent in both Cassava and Plantain flour samples and have been reported to be responsible for compromise in the organoleptic properties of foods. The environment is a key factor in the spread of infectious diseases to people, with different materials acting as mechanical carriers. One cannot overstate the importance of preventing excessive food contamination before processing, using adequate and appropriate food processing methods to prevent contamination during and after foods processing, using quality packaging to preserve foods and reduce health risks, having adequate storage and transportation, and handling finished products in a hygienic manner.