This study surveyed important food crops consumed in Ivory Coast for fungi. To achieve this, the following local food items (attieke, cassava flakes, chili, gnangnan, haricot, melon, millet, okra, rice, white maize and yellow maize) were sampled from local markets (Adjame, Cocody and Youpougon) in Abidjan, Ivory Coast. These food crops were screened for fungal contaminants, and each sample was serially diluted to a concentration of 10−5. One hundred microliters of each mixture at 10−3 10−4 and 10−5 were inoculated onto potato dextrose agar (PDA), Czapek yeast agar (CYA), and malt extract agar (MEA). The isolates were identified using morphological characters and confirmed by PCR with the internal transcribed spacer 1 and 4 primers (ITS1 and ITS4). A total of 227 isolates were morphologically identified and confirmed to be in the genera Aspergillus (54.9%), Penicillium (23.3%) and Fusarium (14.3%). Few isolated species were identified as Alternaria, Chaetomium, Cladosporium, Epicoccum, Emerica, Rhizopus and Trichoderma spp. The highest mean fungal load of 5.9 log10 CFU/g was found in maize. Confirmed isolates were dominated by Aspergillus species which were frequent in cassava flakes, chili, gnangnan, haricot, rice and yellow maize. Penicillium species were found to be frequent in chili, haricot and rice, while Fusarium species highly prevalent in melon and millet. Isolates from food commodities in this study were grouping with known toxigenic fungal species.