Abstract The aim of this study was to establish the differences in fungi and mycotoxin contamination and mycobiota biodiversity between wheat and maize after harvesting. Determination of fungal contamination of wheat and maize is crucial, given that these grains are extensively used in food and feed production. Some moulds can produce toxic secondary metabolites, such as mycotoxins, which can cause serious health problems in humans and animals. Due to the metabolic activities of moulds, undesirable changes in food and feed colour, taste, and smell can occur. In this study, samples of wheat and maize, harvested during 2021 in the Northern Croatia, were analysed for mycological and mycotoxin contamination before storage. Also, potentially mycotoxigenic mould genera were identified at the species level in order to uncover the presence of toxigenic species. The presence of the following mycotoxins was examined: zearalenone, deoxynivalenol, ochratoxin, aflatoxin B1, T-2, and HT-2 toxin. The results indicate that both wheat and maize samples were contaminated with yeasts, with maize exhibiting a higher level of contamination as compared to wheat (1.5 × 104 to 1.8 × 106 vs 1.7 × 103 to 9.0 × 105). In wheat, the predominant mycotoxigenic mould species was Alternaria, as opposed to maize in which the Penicillium genus was the most represented. Mycotoxin analysis revealed that both maize and wheat were contaminated with Fusarium mycotoxins. Aflatoxin B1 and ochratoxin were not determined in any of the tested samples. The results point out that grains carry a different risk of contamination with Fusarium mycotoxins and that maize is more susceptible to fungus spoilage.