A wide range of organisms such as algae, bacteria, fungi and viruses has been documented inside lichens that might be regarded as complex microecosystems where symbionts, parasites and opportunistic species interact. To unravel the diversity of such organisms hidden in lichens thalli, NGS techniques with a deep sequencing are required. The order Arthoniales is a group of predominantly lichenized fungi forming crustose and fruticose thalli, which remain mostly unexplored so far with NGS techniques. The aim of this study is (1) to explore the endolichenic fungal diversity in Arthoniales, and (2) to test if some groups of endolichenic fungi (i. e. Cystobasidiomycetes and Tremellomycetes) are correlated with the thallus complexity (type of thallus, presence/absence of cortex). For this purpose, several lichen thalli from different localities around the world (but essentially from Europe) were collected and used in a MinION Oxford Nanopore Sequencing experiment, using Unique Molecular Index ITS amplicons to build a Native Barcode library. The results showed that the most frequent fungal groups among samples (after their respective primary mycobionts) are Cystobasidiomycetes, Dothideomycetes (principally Capnodiales, Cladosporiales, Dothideales, Mycosphaerellales and Pleosporales), Eurotiomycetes (principally Chaetothyriales), Leotiomycetes and Tremellomycetes, which include a wide range of saprotrophic, endophytic, lichenicolous and phytopathogenic fungi. Cystobasidiomycetes and Tremellomycetes were found in fruticose but also in corticate and ecorticate crustose Arthoniales, but not in all thalli. In conclusion, a wide fungal diversity was found inside Arthoniales thalli but no correlation was found between the presence of Cystobasidiomycetes and thallus complexity.