Phototrophic eukaryotic microalgae and cyanobacteria synthesize both chlorophylls and carotenoids for photosynthesis. Since the pigment compositions are nearly identical across single-cell and macrophytic algae, both types are covered in this chapter. Numerous carotenoids have been identified, and taxonomic studies on algae have been conducted recently. This chapter summarizes the relationship between the distributions of pigments of chlorophylls and carotenoids and the phylogeny of oxygenic phototrophs in marine and freshwater environments, including cyanobacteria, red algae, brown algae, and green algae. These phototrophs contain carotenoids that are specific to their divisions or classes, such as myxol glycoside, fucoxanthin, peridinin, diadinoxanthin, and siphonaxanthin. In addition, carotenogenesis pathways are examined in relation to the chemical structures of carotenoids and the known characteristics of carotenogenesis enzymes in other organisms even though the specific genes and enzymes involved in carotenogenesis in algae remain unidentified. This study provides a summary and update from the first edition on the distribution of major carotenoids, primary carotenogenesis pathways, and the characteristics of carotenogenesis enzymes and genes. It also includes an overview of general identification procedures for carotenoids.