The results of this study revealed that the values of moisture contents significantly increased while ash and carbohydrate were significantly decreased with storage. The change in the crude protein, fat and fiber contents of wheat grain samples were not significantly affected. Alternaria alternata (45.3% of the total propagules) followed by Aspergillus (13.3%) with A. flavus and A. niger (5.42% each) are the most common in freshly harvested wheat grains. Rarely occurred aspergilla include A. candidus, A. fumigatus and A. ochraceus. Rhizopus (1 species, 16.26%) and Mucor (2, 11.82%) followed by Penicillium (1, 4.93%) and Fusarium (3, 3.45%) were also dominant. On the other hand, Aspergillus, Eurotium and Penicillium dominated in stored grains on almost both isolation media. A. flavus, A. niger, E. chevalieri, E. repens, E. rubrum, P. aurantiogriseum, P. chrysogenum and P. expansum were the most common species. With respect to maize grains, A. niger followed by A. flavus were common on both freshly harvested and stored kernels, while Eurotium represented by E. chevalieri and E. rubrum on stored maize only. Total aflatoxin level in all local and imported samples tested was ≤ 10 µg kg-1 using both analytical methods (HPLC and Kits) in both freshly and stored wheat and maize grain samples which is below the permissible limit.