The desert of “La Joya” is considered an analog of Mars due to its hyper-arid conditions, in which very high amounts of radiation are contemplated, sudden changes in temperature between day and night, a very low amount of precipitation and humidity, as well as very noticeable variations in the composition of the soil, which make it difficult for biological material to survive in this area. There are no studies in which extremophilic cyanobacteria species have been reported in the hyper-arid desert of the Pampas de la Joya. In this study, endolithic and epilithic lichens never before studied have been found, which were collected from the desert in the hyper arid region of the Pampas de Joya, for which the isolation and cultivation of the photobionts and mycobionts was carried out. After the purification of the culture, DNA extraction and sequencing of the lichen thallus species was carried out, identifying two species of fungi, Neocatenulostroma microsporum and Acarospora cf. Bullata; both species with 95% homology which is reported as new species. The phylogenetic study of these was carried out, also demonstrating the non-existence of a previous record, giving an idea of the lineage that relates them. A selection of culture medium was carried out in which three culture media (BBM, BG11, and F/2 modified) were tested, determining that the best for its growth was the modified F/2 medium. This is one of the first studies in which the presence of these microorganisms is reported in this hyper-arid desert.