Lichens have a primary role in the biodeterioration of rock substrata and in soil formation. In extreme Antarctic rock-face habitats, their exposed epilithic growth form makes them vulnerable to environmental stress, especially to increased UVB radiation within the late winter ozone “hole”. In this study, FT-Raman spectra of intact epilithic samples of the highly-pigmented lichen species Xanthoria elegans and Xanthoria mawsonii from a continental Antarctic habitat in central Victoria Land and Xanthoria parietina from a maritime temperate location in Scotland have been compared. Vibrational assignments have been made for their pigments, based on parietin and an anthraquinone model. Other significant spectral features are assigned to biodegradative secondary metabolites, cellulose and incorporated substratal rock particles. Differential distribution of parietin pigment bands in the profile of an X. elegans thallus is probably related to the high intensity of UV-radiation reaching its Antarctic cold desert surface environment. The significant differences in Raman spectra between epiphytic X. mawsonii and epilithic X. elegans at the same site possibly indicate different biochemical UV survival strategies. In contrast to spectra from other lichen species studied in our laboratories, the Xanthoria encrustations contain very little calcium oxalate, formed by reaction of oxalic acid with calcareous substrata. The 462 cm−1ν(SiO) band of quartz is found in the Raman spectra from both upper and lower surfaces of the lichen encrustations, confirms the physical incorporation of the substratum into the thallus.