Astaxanthin (3, 3'-dihydroxy-β,β-carotene-4,4'-dione) is a high-value ketocarotenoid synthesized by several species of microalgae, plants, bacteria, and fungi and widely used as a potent antioxidant for human health and also a coloring agent. About six genes (CrtI, CrtL, CrtO, CrtW, CrtR and CrtZ) involve in the biosynthesis of astaxanthin. Phylogenetic analysis of astaxanthin biosynthetic pathway genes and their evolutionary rate variations has been studied among major phylogenetic groups of organisms such as plant, algae, and bacteria. The maximum likelihood (ML) algorithm was used in protein coding DNA sequences to infer the evolutionary relationship for the Crt genes among different eukaryotic and prokaryotic lineages. The phylogenetic analysis suggests that evolutionary pattern of Crt genes in eukaryotic and prokaryotic is characterized by even such as lateral gene transfer and gene duplication events. The specific amino acids present in the respective enzymes are the reason for their functional divergence. The dN values indicate that astaxanthin biosynthetic genes are more conserved in plant and algae than in any other bacterial phyla. This study provides the knowledge of individual Crt enzymes in different organisms that helps to increase the production of astaxanthin which is a biologically significant apocarotenoid that has various uses ranging from human health to cosmetic purposes. © 2016 Elsevier B.V.