To elucidate the biosynthetic pathways of carotenoids, especially myxol 2-glycosides, in cyanobacteria, Anabaena sp. strain PCC 7120 (also known as Nostoc sp. strain PCC 7120) and Synechocystis sp. strain PCC 6803 deletion mutants lacking selected proposed carotenoid biosynthesis enzymes and GDP-fucose synthase (WcaG), which is required for myxol 2-fucoside production, were analyzed. The carotenoids in these mutants were identified using high-performance liquid chromatography, field desorption mass spectrometry, and Cyanobacteria synthesize carotenoids, as do all phototrophic organisms. The carotenoids in cyanobacteria are not limited to just the common carotenoids, such as -carotene, but also include some unique ketocarotenoids and carotenoid glycosides, which are not found in higher plants (6). It has become evident from several recent studies that these unique carotenoids are different in different cyanobacterial species, and cyanobacteria can be classified into several groups based on their unique carotenoids (39). Members of the first group, which includes the genera Anabaena and Nostoc, contain -carotene, keto derivatives of -carotene such as echinenone, and myxol glycosides, but little or no zeaxanthin. Members of the second group, including Synechocystis sp. strain PCC 6803 and Thermosynechococcus elongatus strain BP-1, contain these carotenoids as well as zeaxanthin. Members of the third group, which includes the genera Synechococcus and Prochlorococcus, contain -carotene, zeaxanthin, and nostoxanthin but lack both ketocarotenoids and carotenoid glycosides. Prochlorococcus also contains ␣-carotene, and the lycopene cyclases in these genera have homology to those of plants.We recently identified the molecular structures of carotenoids in some Anabaena and Nostoc strains, and we proposed carotenogenesis pathways and genes (37,38). In these genera, the major carotenoids were -carotene and echinenone, and the polar carotenoids were myxol and 4-ketomyxol glycosides.