Abstract The principles of taxonomy, chemotaxonomy and chemosystematics are outlined. Chemosystematics may serve to improve existing classification of organisms by revealing phenetic and phylogenetic relationships. Secondary metabolites hitherto studied for chemosystematic purpose are mentioned. Additional knowledge of biosynthetic pathways leading to the terminal products is a better proof of phylogeny and differentiation. For microorganisms with restricted morphological character, chemosystematics forms an important taxonomic tool. Properties of carotenoids which favour their use as chemosystematic markers are discussed, and the carotenoids of photosynthetic and other bacteria, yeasts and other fungi, algae and higher plants are discussed separately, in light of available structural evidence and known or postulated biosynthetic pathways. Systematic changes in structural features of the terminal carotenoid products correlate well with commonly accepted phylogenetic trees. Particularly within photosynthetic bacteria, algae, yeasts and fungi carotenoids are considered a useful tool in classification. In lower animals carotenoid analysis may demonstrate food chain relationship and specific metabolic capacity. Future prospects for use of carotenoids in classification are considered.
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