Black fungi are among the most stress-tolerant eukaryotic microorganisms. Though they share morphological similarities, they often hide great genetic diversity and present multiple life-styles. Lichenothelia and Saxomyces are two genera for which insights in the ecology and phylogenetic relationships within the class Dothideomycetes have been recently revealed. Here we expanded the taxon sampling and added new taxa, from multiple habitats, to previous datasets to better resolve and support their independent identity. Environmental samples and culture isolates have been DNA-extracted and sequenced by Sanger sequencing to produce a strong multilocus phylogeny. Furthermore, the axenically isolated fungi of both Saxomyces and Lichenothelia have been used to set co-cultures with algal strains (Trebouxia spp. and Coccomyxa sp.) previously isolated from different lichen thalli. By doing this we aim at inducing possible formation of lichen-like or less organized structures and to improve our knowledge about the trophic pathways of these particularly oligotrophic fungi. Our molecular phylogeny and culture experiment show to which extend black fungi underwent convergent evolution and are related to lichenized fungi and fungi presenting different life-styles.