For activity and survival in extreme terrestrial Antarctic habitats, lithobiontic cyanobacteria depend on key biomolecules for protection against environmental stress and for optimization of growth conditions. Their ability to synthesize such molecules is central to their pioneering characteristics and major role as primary producers in Antarctic desert habitats. Pigmentation is especially important in protecting them against enhanced UVB damage during stratospheric ozone depletion (the Ozone Hole) during the Antarctic spring and subsequent photoinhibition in the intense insolation of the summer. To be effective, especially for the screening of highly shade-adapted photosystems of cyanobacteria, protective pigments need to be located strategically. Antarctic lithic cyanobacterial communities are therefore stratified, as in soil biofilms of Alexander Island, the benthic stromatolitic mats of ice-covered hypersaline lakes in the McMurdo Dry Valleys, and the endolithic communities within translucent Beacon sandstone outcrops of Victoria Land. The protective pigments include scytonemin, carotenoids, anthroquinones and mycosporine-like amino acids. To detect and locate photoprotective pigments in situ in free-living cyanobacteria and cyanolichens from hot and cold desert habitats, we have used Fourier-transform Raman micro-spectroscopy. With appropriate power inputs for labile molecules, this high-precision, non-intrusive laser-based technique can not only identify biomolecules in their natural state but also locate them spatially within the habitat relative to the components of the community, which require protection. In conjunction with direct and epifluorescence microscopy it provides a spatial and functional description of the protective strategy of a community. We present the unique Raman spectrum of scytonemin and use its primary and corroborative peaks to identify it within the plethora of other biochemical constituents of several natural cyanobacterial communities, including an Antarctic endolith. The remote-sensing aspect of this technique makes it suitable not only for spatial biochemical analysis of present and palaeontological Antarctic communities but also for analogous putative habitats on Mars.