Black fungi are among the most stress tolerant organisms on Earth. In this study prote-omics of black rock microcolonial fungi and pathogenic black yeasts was performed in order to evaluate the impact of temperature on the protein expression profile. 2D-protein patterns of Knufia perforans, Exophiala jeanselmei and Friedmanniomyces endolithicus were compared with the hyphomycete Penicillium chrysogenum. Whereas P. chryso-genum showed the highest number of protein spots at 40C and the lowest at 1C, thus exhibiting real signs of temperature induced reaction, black fungi when exposed to temperatures far above their growth optimum decreased the spots number indicating a down-regulation of the metabolism. At 1C, an increase of protein spots occurred instead in all the black fungi strains. These results indicate a rather different strategy to cope with non-optimal temperature in rock inhabiting black fungi than in hyphomycetes as P. chrysogenum. 2D-DIGE was applied for characterization of temperature-related chang-es in total protein spot abundance in the black yeast Exophiala dermatitidis, an agent of primary and secondary diseases in both immunocompromised and healthy humans. Three incubation temperatures (37, 45, 1C) and two time spans (1h, 1 week) were se-lected to simulate different environmental conditions and evaluate the effects of short- and long-term exposure. A total of 32 variable proteins were identified by mass spec-trometry. Data about protein functions, localization and pathways were obtained. Inter-estingly, a typical stress response under non-optimal temperature was not observed at the proteome level, whereas a reduction of the metabolic activity was detected after ex-posure to cold. Our results suggests that under increased temperatures, a fine regulation of protein expression takes place, particularly concerning the protein sets which are in-volved in crucial biological processes, to guarantee the cell survival and maintenance.