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The Fourier-transform Raman spectra of desert varnish specimens and their rock substrata from locations in Colorado and Nevada, USA, are reported. The Colorado specimen exhibits molecular signatures for beta-carotene and scytonemin; the latter is a characteristic biomarker of cyanobacterial colonies and is produced by these organisms in response to high UV-radiation stress. The Nevada specimen, on the other hand, exhibited characteristic Raman bands arising from whewellite and lichen metabolites such as atranorin and paretin, indicative of an epilithic lichen colonization. The application of Raman microscopy for the identification of extinct or extant biological colonization of rocks in exposed hot desert environments could form a useful adjunct for database construction relevant to exobiological studies and key spectral bioindicators for the robotic exploration of planetary surfaces. Copyright (C) 2004 John Wiley Sons, Ltd.