Fungi with dark-coloured mycelia - also known as black fungi - form a ubiquitous fraction of microbial communities on rock surfaces all over the world. These organisms show a high capacity to adapt to a wide range of ecological conditions, including those peculiar of extreme environments. Their high tolerance to multiple abiotic stresses, such as solar radiation and osmotic stress is assured by the production of melanin pigments and osmoprotective compounds. The cosmopolitan genera Lichenothelia and Saxomyces were taken as iconic representatives of polyextremotolerant rock-inhabiting black fungi. I investigated their phylogenetic relationships with an extended taxon sampling within the class Dothideomycetes, the most diverse and life-style rich fungal class in Ascomycota. The three loci phylogenetic inference I set up, considering both environmental samples and culture isolates, highlighted the paraphyly of the two genera. The integrative taxonomy approach based on morphological as well as phylogenetic evidences allowed the taxonomical revision of the genera and the description of three new taxa. Rock inhabiting fungi often share substrata with green algae and cyanobacteria and some of them are associated with lichen thalli. Lichenothelia is of a particular interest because it includes lichen parasites and species which are loosely associated with algae or which grow independently on rock. Given their life style plasticity, we chose it for an in vitro culture experiment, studying the development of three Lichenothelia species when co-cultured with two different subaerial algae isolated from lichens (i.e., lichen photobionts). The results showed that the presence of algae neither influence the growth rate of fungi nor the formation of any lichen-like structure. However, this standardized approach proved suitable for future investigations on fungal-algal interactions in other systems. Previous multi-locus phylogenies of Dothideomycetes have investigated evolutionary relationships at order and family level within the class but they often failed to resolve the early diverging nodes, which were generating inconsistent placements of some clades. Here, I applied a phylogenomic approach to resolve relationships in Dothideomycetes, adding the newly sequenced Lichenothelia and Saxomyces genomes, to a wide dataset comprised of 238 individuals. I explored the influence of tree inference methods, supermatrix vs. coalescent-based species tree, and the impact of varying amounts of genomic data. The phylogenomic reconstructions, based on up to three thousand genes, provide well-supported topologies for Dothideomycetes, recovering Lichenothelia and Saxomyces among the earliest diverging lineages in the class together with other rock inhabiting fungi and lichens and thus, suggesting the rock-inhabiting life style as ancestral in the class. Further studies will be necessary to shed light on the molecular bases of stress tolerance and latent capacity of establishing symbiosis of these fungi.