Over the past few years, endolichenic fungi discovery are constantly increasing. In 2016, Spribille et al. discovered a species of Cystobasidiomycetes, living in the cortex of Bryoria fremontii and other yeasts species of the same group in several lichens, hypothesizing that these fungi could be ubiquitous, and that some of them might play a role in the cortex architecture and even be responsible for the appearance of foliose thalli in the Parmeliaceae family. Conversely, Lendemer et al. (2019) only found endolichenic fungi in 2.7% of their samples. In the present study, we investigated the presence of these basidiomycete yeasts in the Arthoniales order and tested whether a difference can be observed between corticate and ecorticate thalli, and between crustose and fruticose thalli. A preliminary study has been carried out on a limited number of samples. DNA was extracted via the CTAB protocol and sequenced using MinION (Oxford Nanopore) to obtain ITS sequences from Cystobasidiomycetes. The Ligation Sequencing Amplicons Native Barcoding technique was applied. It proved to be an excellent technique as it allowed to obtain both high quality sequences of the mycobiont and the photobiont (with some exceptions) and also casually occurring contaminants in small amount such as pollens and other fungi. However, no Cystobasidiomycetes were found, independently from the thallus growth form or the presence of a cortex. These preliminary results seem to confirm the conclusions of Lendemer et al., i. e. Cystobasidiomycetes are not as ubiquitous as we thought. These preliminary results are in contrast with the hypothesis of Spribille et al. about their potential role in the cortex architecture. To better support our findings a larger number of samples are needed, in order to cover more lichenized lineages and make the results robust.