One‐hundred maize samples were analyzed for fungal contamination using conventional and molecular methods. The percentage incidence of different genera isolated revealed the predominance of Fusarium (82%), Penicillium (63%), and Aspergillus species (33%) compared to other genera. Fusarium occurred in 90% and 74% of small scale and commercial samples, respectively, while Penicillium occurred in small scale and commercial samples at an incidence rate of 64% and 62%, respectively. However, among the species, Fusarium verticilloides have the highest incidence of 70% and 76% in commercial and small‐scale maize, respectively, while Penicillium digitatum has 56% total incidence. Aspergillus fumigatus (27%) were also the most dominant of these genera. Fungal genera isolated included Alternaria and Cladosporium although occurring at a lower incidence level of 30%, 32% and 16%, 20%, respectively, in small‐scale and commercial samples. The results emphasize that farmers and consumers should be alerted to the danger of fungal contamination in maize.