We investigated the mycobiota of nests and food channel of Microcerotermes cf. strunckii and verified if there are differences in the mycotic constitution among the analyzed materials. We collected the studied materials in fragments of semi-deciduous forest in the municipality of Anápolis (Brazil). Five activated nests were evaluated, besides the food channel of 11 workers in each of the sampled nests. The nests samples and the workers were seeded in Petri dishes in growth medium of Potato Dextrose Agar (PDA), which were incubated in 25ºC during six days. Posteriorly, the fungal colonies were purified and identified. Seventeen fungal taxa were registered, in which Paecilomyces variotii, Penicillium frequentans and Aspergillus flavus were the most frequent species in the nest material and P. variotii and A. flavus, the most common in the food channel. The fungal diversity found in the nests and in the food channel of M. cf. strunckii in the Cerrado can be considered high when compared to similar studies with the same genus in areas of the Caatinga biome. The mycobiota registered in nests and in the alimentary canal of workers were also observed in the termite mound material. This is the first study addressing the mycobiota associated to termites in the Cerrado biome and has demonstrated the presence of Ascomycetes fungi with lignocellulosic properties, resulting in possible interactions of M. cf. strunckii and fungi.