Elucidating the complex relationship between plants and endophytic fungi is very important in order to understand the maintenance of biodiversity, equity, stability, and ecosystem functioning. However, knowledge about the diversity of endophytic fungi from species of the native Brazilian Cerrado biome is poorly documented and remains largely unknown. These gaps led us to characterize the diversity of Cerrado endophytic foliar fungi associated with six woody species (Caryocar brasiliense,Dalbergia miscolobium,Leptolobium dasycarpum,Qualea parviflora,Ouratea hexasperma, andStyrax ferrugineus). Additionally, we investigated the influence of host plant identities on the structure of fungal communities. Culture-dependent methods coupled with DNA metabarcoding were employed. Irrespective of the approach, the phylumAscomycotaand the classesDothideomycetesandSordariomyceteswere dominant. Using the cultivation-dependent method, 114 isolates were recovered from all the host species and classified into more than 20 genera and 50 species. Over 50 of the isolates belonged to the genusDiaporthe, and were distributed into more than 20 species. Metabarcoding revealed the phylaChytridiomycota,Glomeromycota,Monoblepharomycota,Mortierellomycota,Olpidiomycota,Rozellomycota, andZoopagomycota. These groups are reported for the first time as components of the endophytic mycobiome of Cerrado plant species. In total, 400 genera were found in all host species. A unique leaf endophytic mycobiome was identified in each host species, which differed not only by the distribution of fungal species, but also by the abundance of shared species. These findings highlight the importance of the Brazilian Cerrado as a reservoir of microbial species, and emphasize how endophytic fungal communities are diversified and adapted.