Chagas is a neglected disease, one of Brazil’s main medical and social problems and a serious public health problem in the Americas, with more recent occurrences in non-endemic countries outside of the Americas. Research into the microbiota of triatomines is relevant because of its potential role in vector competence and as a proposed biological control strategy. Stressing a possible insect-fungal interaction in the development of Trypanosoma cruzi, and considering the lack of studies on the subject, we analyzed the fungal microbiota of the digestive tract of two species considered important vectors of Trypanosoma cruzi: Triatoma infestans and Panstrongylus megistus. Specimens were dissected, digestive tracts macerated and contents serially diluted. Each aliquot was seeded in three culture media. The plates were incubated in type B.O.D. climate chambers for 21 days, after which isolated colonies were morphological characterized and identified. There have been few published studies on the fungal microbiota of the triatomine digestive tract. Comparing the results found here with existing data reveals that the genera Aspergillus and Penicillium are commonly found in the digestive tract of the studied triatomines. Among the several genera identified, the species found in the highest percentages were Aspergillus flavus, Paecilomyces variotii, Penicillium waksmanii, Penicillium raistrickii and Penicillium fellutanum. Quantitative differences in the number of isolated fungal strains were observed according to sex and nymphal stage of the vector. The present findings corroborate those found in the literature, showing that there is a natural fungal microbiota in triatomines. Data revealing quantitative differences in isolated fungal strains found in male, female and nymphs reinforce the idea that their presence is related to physiology and fasting resistance. The secondary metabolite-producing fungi isolated in this work have in their biology great potential to be tested with regard to the establishment of T. cruzi in the digestive tract of its vector.