A compact handheld Raman spectrometer equipped with a 532 nm excitation laser was used to detect pigments as possible biomarkers in autotrophic (cyanobacteria and purple sulfur bacteria) and heterotrophic halophilic microorganisms (Archaea of the family Halobacteriaceae, Salinibacter). Common as well as less common carotenoids, including α-bacterioruberin, salinixanthin, and spirilloxanthin derivatives were detected in cell pellets of model organisms belonging to the genera Haloferax, Haloarcula, Halobacterium (Archaea), Salinibacter (Bacteroidetes), and Ectothiorhodospira (Gammaproteobacteria). Direct measurements on such cultures provide fast and reliable identification of pigments. Bacterioruberin was detected as the dominant carotenoid in pellets of cells collected from the saltern crystallizer ponds in Eilat, Israel. Raman analysis of the colored layered microbial communities in a benthic gypsum crust in the saltern evaporation ponds showed signals consistent with the presence of myxoxanthophyll and echinenone carotenoids in the upper orange and dark-green cyanobacterial layers. Chlorophyll a and phycocyanin expected in the green layer were not detected using the green excitation. Spirilloxanthin dominates the red layer below, inhabited mainly by purple sulfur bacteria. To our best knowledge, this is the first attempt to detect and identify pigments in natural microbial communities consisting of different types of halophilic microorganisms by direct Raman spectrometric measurements using light compact handheld devices. Copyright © 2013 John Wiley & Sons, Ltd.