A small sulphide-rich waste-rock dump from the derelict Libiola mine (eastern Liguria, Italy) was studied for evaluating the fungal richness as well as the correlation among microfungi and lithology, mineralogy, and contaminants. The waste-rock dump is characterized by severe environmental conditions in particular for the (1) high metal and sulphur contents, (2) presence of reactive sulphides (mainly pyrite) triggering acid mine drainage processes, (3) acid-to-strong acid pH values, and (4) high cementation grade of the sediments evolving up to hardpans. Despite these critical and dangerous environmental conditions, a total of 603 CFUs belonging to 30 filamentous fungal species were isolated. Correlations analyses underlined that serpentinite-rich samples resulted particularly poor of fungal richness, with respect to sulphide-mineralized basalts. Only some Penicillium species, in fact, resulted adapted to survive in serpentinitic samples. Finally, among the isolated species, Cladosporium cladosporioides, C. iridis, C. tenuissimum, Metarhizium anisopliae, Penicillium brevicompactum, P. expansum, and Phanerochaete sordida appeared particularly well adapted to the extreme edaphic conditions of the Libiola mine. These results allowed the selection of particularly adapted and tolerant fungal strains usable in biotechnological processes for bioremediation.