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Background: Pearl millets are a group of highly variable small-seeded grasses; they are widely grown around the world as cereal crops and have a wide array of uses. They harbor a lot of fungi from field to post-harvest which are capable of posing health hazards to humans and animals. The objectives of this research study were to isolate and identify different fungi associated with millet at different periods of storage and determine their mycotoxin profile. Materials and Methods: Millet samples were purchased randomly from vendors in three major markets situated in three different local governments in Ibadan, Oyo State, Nigeria over a three-month period. The samples were brought to the laboratory in sterile polythene bags. Isolation of fungi from the millet samples was done by direct plating on Saboraud's Dextrose Agar (SDA) incorporated with chloramphenicol to prevent bacterial growth. The plates were incubated at room temperature for 48-72 hours and observed. Results: Pure cultures of fungi were obtained by repeated sub-culturing. A total of fourteen (14) fungi belonging to twelve (12) genera were obtained. Aspergillus fumigatus had the highest (25.7%) frequency of occurrence, with Syncephalastrum spp (6.5%), Rhizopus spp (5.7%), Fusarium spp (3.6%), Alternaria brassicicola (2.8%), Curvularia spp (3.2%), Mucor mucedo (2.4%), Gonatobotrys simplex (1.2%), Acladium conspersum (0.5%), Penicillium spp (2.8%), Aspergillus niger (21.2%), Aspergillus flavus (23.6%) while Nigrospora oryzae and Sporendonema spp had the lowest (0.4%) frequencies. The mycotoxin profile quantification revealed the presence of four aflatoxins: AFB1, AFB2, AFG1 and AFG2 in the millet samples with the samples purchased from Oje having the highest aflatoxin level of 897 ppb. Conclusion: There is the need to adopt strict hygiene, storage and preservative practices to prevent fungi from infecting millet samples with a view to controlling their aflatoxin level.