Endophytes microorganisms have the potential to control vascular diseases caused by Fusarium spp. which does not have an effective chemical control. In this study, endophytes populations present in Manzano -apple bananas- affected by Fusarium oxysporum f. sp. cubense race 1 were studied. Endophytes were isolated in two commercial farms in Urabá-Colombia, taking leaf, pseudostem, corm and root tissues from healthy and diseased plants. Two disinfestation methods were used: conventional (2% hypochlorite + 70% Ethanol) and chlorine gas (6.25% sodium hypochlorite + 37% hydrochloric acid). 143 isolates with 11 genera were obtained from healthy plants with the following frequencies: Fusarium sp. (18.67%), Nigrospora sp. (8%), mycelia sterilia (48%), among others. Also, eight genera were found in diseased plants, Fusarium sp. (23.53%), Colletotrichum sp. (17.76%), mycelia sterilia (47.06%). All endophytic fungi are ascomycetes, except for Pythium sp., oomycete that was isolated only from diseased plants.  Pythium sp. which, was isolated from healthy plants, constitutes the first reports in musaceas. According to the Simpson and Shannon-Wiener diversity indices, a higher diversity of fungi was found in healthy plants (0.282 and 1.729) than in infected ones (0.294 and 1.532); it depends on disinfection method as demonstrated here, suggesting that tissue cleaning and disinfection methodologies modulate the microbial populations obtained.  This work contrasted endophytic fungi in symptomatic plants attacked by Foc R1 with healthy plants and also the genus of endophytic fungi described in this study have already been reported in previous research in Musa, except for the oomycete Pythium Key words: Biological control, diversity, Foc, microbiota, vascular disease. &nbsp