Fusarium is a ubiquitous mycotoxigenic genus of filamentous fungi. Members of this genus cause devastating plant diseases on various cereal grains such as maize, rice, wheat, and sorghum. Maize (Zea mays) is the most widely produced cereal grain globally, with over 1.2 billion tons produced in 2019 (FAO, 2020). In Southern Africa, maize is a staple food that is consumed by more than 70% of the population, however Fusarium species cause many diseases on maize and subsequently reduces grain yield and quality. The additional health risks posed by mycotoxins greatly impacts both the health system as well as the food industry. Teff (Eragrostis tef) is a cereal grain that is primarily used as animal feed and a staple food consumed by humans in East Africa. There is limited knowledge on Fusarium species diversity, and the impact of such species, on teff. This study aimed to investigate the species diversity of Fusarium from asymptomatic transgenic maize intended for human consumption, as well as teff. A total of 102 Fusarium-like isolates were identified morphologically. Diagnosis was established by using polymerase chain reaction of fungal DNA, followed by sequencing portions of translation elongation factor 1 alpha (TEF-1α), RNA polymerase second largest subunit (RPB2), calmodulin (CAL) and beta-tubulin (β-TUB). The multi-locus maximum likelihood phylogenies revealed 80 Fusarium isolates. The isolates consisted of five species complexes, namely the Fusarium sambucinum -, incarnatum-equiseti -, fujikuroi -, oxysporum -, and chlamydosporum species complexes. Some recovered species are known to be pathogenic and mycotoxigenic, such as Fusarium verticillioides, F. temperatum, F. boothii, F. subglutinans, and F. nygamai. This study has resulted in the first report of many species on maize and teff in South Africa and widened our understanding of this genus and its distribution as well as its association with maize and teff. The co-occurrence of various Fusarium species from each plant was observed, raising the possibility of various cocktails of mycotoxins present on these plants. Further phylogenetic analysis resulted in the description of one novel Fusarium species (Fusarium iowaense prov. nom.) within the main African clade of the FFSC.