This study aimed at isolation and identification of fungi associated with packaged and unpackaged cereal flour sold within Ikot Ekpene metropolis. The cereal samples used in this study were; wheat flour, corn flour and soya bean flour and were obtained from (Urua Otoh) and Urua Mbakara) for fungal analysis using standard procedures. The result obtained showed the highest fungal count in samples from (Urua Otoh) (corn flour) with the total fungal count of 7 x 104Cfu/g and 9 x 105Cfu/g for the packaged and unpackaged samples respectively. The lowest fungal count was observed in samples from (Urua mbakara) (soybean) with the total fungal count of 2 x 104Cfu/g and 3×105Cfu/g for the packages and unpackaged samples respectively. The fungal isolated were of the genera Aspergillus sp., Mucor sp. and Penicillium sp. Aspergillus sp. recorded the highest percentage occurrence which ranged from 46.7% – 30.0% and penicillium sp recorded the lowest percentage occurrence which ranged from 45.0% – 13.3%. the presence of these fungi in food are known to produce different mycotoxins and according to WHO, the maximum level of aflatoxin in cereals is between the range of 0.5µg – 15µg/kg. In comparison to this study, the unpackaged cereal flour samples were contaminated and will cause harmful effect to human health if consumed. Therefore production line should be monitored to ensure good manufacturing and good handling practice.