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Six endolithic communities from Antarctic cold desert environments have been analysed by Raman spectroscopy. The extreme conditions that the organisms have to withstand in cold environments leads to the adoption of different survival strategies and adaptation of the geological environment. Production of radiation- and desiccation-protective biomolecules is identifiable but the displacement of potentially protective minerals onto the rock surface has also been detected as a protective mechanism against UV-radiation. In this work, Raman spectroscopy is demonstrated as a valuable technique to determine the organic and inorganic compounds used by microorganisms as protective mechanisms against extreme stress conditions. The data from this study will be useful for construction of molecular recognition biomarkers and remote Raman spectral sensing experiments proposed for terrestrial extremophiles in stressed environments.