The microcolonial black fungus Cryomyces antarcticus is an extremophile organism growing on and in rock in the Antarctic desert. Ecological plasticity and stress tolerance make it a perfect model organism for astrobiology. 2D-gel electrophoresis and MALDI-TOF/TOF mass spectrometry were performed to explore the protein repertoire, which allows the fungus to survive in the harsh environment. Only a limited number of proteins could be identified by using sequence homologies in public databases. Due to the rather low identification rate by sequence homology, this study reveals that a major part of the proteome of C. antarcticus varies significantly from other fungal species.