Many new carotenoid synthesis genes have recently been identified through genomic sequencing or functional cloning. Some of them exhibit novel structures and/or novel functions. This review describes such examples in the families of lycopene beta-cyclases, putative homologues of phytoene dehydrogenases and new carotenoid hydroxylases. Both the functionally novel lycopene beta-monocyclases and structurally novel fusion-type of lycopene beta-cyclases were described. Another newly discovered sequence of lycopene beta-cyclase described might represent a new class of lycopene beta-cyclases previously not identified in several cyanobacteria. Three examples of putative homologues of phytoene dehydrogenases were described, however, they were confirmed to encode different and/or new functions such as beta-carotene ketolase, 4,4'-diapolycopene oxygenase or prolycopene isomerase. Two new carotenoid hydroxylase genes were described that encoded the new function of 2,2'-beta-ionone ring hydroxylase or 3,3'-isorenieratene hydroxylase. Phylogenetic analysis of these genes shed light on their possible evolutionary origins. These new genes also provide tools for synthesis of novel and desirable carotenoids by genetic engineering.