Contamination of maize adversely affects maize quality, yield, and export creating a gap in the attainment of food security, which is a millenium development goal in Nigeria. The study determined fungal abundance, genetic variability, and prevalence of toxigenic fungi in maize grains consumed in North Central, Nigeria. Sixty composite stored maize samples were collected and fungi were isolated and identified after which a multiplex polymerase chain reaction was used to confirm the presence of mycotoxin regulatory genes in suspected toxigenic fungi. The genetic relationship among the toxigenic fungi was determined and the genetic correlation between Aspergillus isolates was established through Restriction fragment length polymorphism (RFLP) analysis. About 389 (64.83%) of the total maize samples collected had fungal species belonging to the genera Aspergillus, Mucor, Penicillium, Fusarium, Trichophyton, and Talaromyces associated with them. Among the regions surveyed, Kogi State exhibited the highest maize contamination rate at 89 samples, accounting for 22.9% of the total samples collected. In Benue and Kogi, the genus Aspergillus exhibited the highest relative abundance, with percentages of 76.6% and 76.3%, respectively. Among its species, Aspergillus flavus and A. niger were the most predominant. Kwara State had the highest fungal diversity with a value of 1.711 ( P < .05). Benue State had 11 isolates (4.6%) with genes encoding for mycotoxin production, the highest recorded. Conversely, Nasarawa and Niger States each had the lowest count, with 4 isolates possessing such genes. Out of the 238 fungi suspected to be mycotoxigenic that were isolated, 39 have genes that encode for mycotoxin synthesis. Low divergence existed between toxigenic fungal species using the alpha diversity index. This study confirmed that the grains were contaminated with closely related fungal strains, and concluded that maize grains consumed in North Central Nigeria showed high association with fungal microbiota, including species capable of contaminating the grains with mycotoxins