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As part of a worldwide sampling nine black fungi were isolated from rocks collected in four distinct sites of the Alps at high altitudes. Based on a nucSSU, nucLSU and mtSSU multi-locus phylogeny, seven of them were found to cluster into a distinct and well-supported clade in a basal position within the Class Dothideomycetes. As in other rock fungi these new groups of isolates were characterized by a meristematic growth and a scarcely differentiated morphology with highly melanized and thick-walled toruloid hyphae. Nonetheless, few peculiar characters were also observed as convoluted hyphal tips and the production of spherical propagules. The new genus and species Saxomyces alpinus and S. penninicus, are here described based on morphological and molecular data, in a yet to be defined order of the Dothideomycetes. The remaining two black fungi clustered in Cryomyces, a genus previously exclusively found in rocks from the McMurdo Dry Valleys in Antarctica. These two isolates were genetically distant from other Antarctic Cryomyces species based on ITS sequences, and they showed a peculiar morphology; they are here described as the new species C. montanus and C. funiculosus. Implications of our results on the evolution, adaptation and dispersal of rock-inhabiting fungi under extreme conditions are discussed.