We identified the molecular structures, including the stereochemistry, of all carotenoids in Thermosynechococcus elongatus strain BP-1. The major carotenoid was -carotene, and its hydroxyl derivatives of (3R)--cryptoxanthin, (3R,3R)-zeaxanthin, (2R,3R,3R)-caloxanthin and (2R,3R,2R,3R)-nostoxanthin were also identified. The myxol glycosides were identified as (3R,2S)-myxol 2-fucoside and (2R,3R,2S)-2-hydroxymyxol 2-fucoside. 2-Hydroxymyxol 2-fucoside is a novel carotenoid, and similar carotenoids of 4-hydroxymyxol glycosides were previously named aphanizophyll. Ketocarotenoids, such as echinenone and 4-ketomyxol, which are unique carotenoids in cyanobacteria, were absent, and genes coding for both -carotene ketolases, crtO and crtW, were absent in the genome. From a homology search, the Tlr1917 amino acid sequence was found to be 41 identical to 2,2- -hydroxylase (CrtG) from Brevundimonas sp. SD212, which produces nostoxanthin from zeaxanthin. In the crtG disruptant mutant, 2-hydroxymyxol 2-fucoside, caloxanthin and nostoxanthin were absent, and the levels of both myxol 2-fucoside and zeaxanthin were higher. Therefore, the gene has a CrtG function for both myxol to 2-hydroxymyxol and zeaxanthin to nostoxanthin. This is the first functional identification of CrtG in cyanobacteria. We also investigated the distribution of crtG-like genes, and 2-hydroxymyxol and/or nostoxanthin, in cyanobacteria. Based on the identification of the carotenoids and the completion of the entire nucleotide sequence of the genome in T. elongatus, we propose a biosynthetic pathway of the carotenoids and the corresponding genes and enzymes.