Lichen mycobionts contain inside their thalli, in addition to their photobiont, a wide range of other organisms such as bacteria, viruses or other fungi and algae. These organisms are not necessarily part of the symbiosis, but also opportunistic species. NGS techniques with a deep sequencing have been used to explore the diversity of such organisms present in these microecosystem represented by lichens thalli. The aim of this study is (1) to explore the fungal diversity in the lichen order Arthoniales, a group that harbour crustose and fruticose thalli and unexplored so far with NGS techniques, and (2) to find particular Cystobasidiomycetes in the same order, which are supposed, according to a previous study on Parmeliaceae (Lecanorales), to have a role in the thallus complexity and cortex structure. For this purpose, 93 lichen thalli from different localities around the world were collected and used in a MinION Oxford Nanopore Sequencing experiment, using Unique Molecular Index ITS amplicons to build a Native Barcode library. Results showed that the most recurrent groups among samples (after their respective primary mycobionts and photobionts) are Chaetothyriales, Capnodiales and Helotiales, which include a wide range of endophytic, saprotrophic and phytopathogenic fungi. Other less frequent groups are Cystobasidiomycetes, Lichenostigmatales, Mycosphaerellales, Pleosporales and Tremellales. Cystobasidiomycetes 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 the thallus types or cortex.