A great diversity of pigments is produced by different groups of prokaroytes. Some pigments serve to convert light energy into biologically available energy: chlorophyll a for oxygenic photosynthesis in cyanobacteria, bacteriochlorophylls in anoxygenic phototrophs, retinal pigments such as bacteriorhodopsin and xanthorhodopsin. Phototrophic prokaryotes generally also contain accessory pigments involved in light harvesting: the phycobiliproteins of the cyanobacteria, carotenoid pigments in all oxygenic and anoxygenic phototrophs. Carotenoids are also widespread among the non-phototrophic prokaryotes, where they may protect the cells from radiation damage. Many other classes of pigments are found: the yellow-orange to pink flexirubins of some members of the Bacteroidetes, the yellow xanthomonadins of the genus Xanthomonas, the purple violacein of Chromobacterium violaceum, the fluorescent pyoverdin and the blue pyocyanin of Pseudomonas spp., the red prodigiosin of Serratia marcescens and others. This chapter provides an overview of these pigments and the methods used for their extraction, separation and spectroscopical and chemical characterization. Examples are given of the use of pigments as differential characteristics in the taxonomy and classification of prokaryotes.