The diversity of endophytes and their ecological relationships with the endangered conifer Araucaria angustifolia (a critically endangered species) are unrevealed. This study aimed to characterize the diversity of endophytic fungi associated with A. angustifolia. To this end, we analyzed 90 fragments from five individuals collected from a mixed localized fragment in Guarapuava-PR, Brazil. The total DNA of 61 morphotypes was extracted and the Internal Transcribed Spacer (ITS) region was amplified and sequenced. The sequence analysis allowed the identification of 37 genera belonging to the phylum Ascomycota and the classes Eurotiomycetes, Dothideomycetes, and Sordariomycetes, divided into 11 orders and 13 families. Most of the isolated fungi belonged to the Sordariomycetes class (40%) and to the Xylaria genus (14%), while Eurotiomycetes was the minority class within the community. Our results reveal the high endophytic richness supporting the life cycle of A. angustifolia and reinforce the necessity for the conservation of this conifer, as many genetic resources can be lost owing to its irrational exploration.