Carotenoids, as a group of over 700 valuable unsaturated terpene compounds classified as carotene and xanthophyll family, are endowed with powerful nutritional value. Phytoene dehydrogenase is the key rate-limiting enzyme in carotenoids biosynthesis pathway, involved in catalyzing the conversion from colorless hydrocarbon phytoene to other pigmented carotenoids, and plays an essential central regulation role. The function of phytoene dehydrogenases from different organisms exist diversity. CrtP, CrtQ and isomerase CrtH are essential for the formation of lycopene in most Cyanobacteria, whereas PDS, ZDS and isomerase Z-ISO, CrtISO are in charge of producing lycopene in most algae and plants. Nevertheless, there is only one CrtI-type for the formation of neurosporene, lycopene or dehydrolycopene in most bacteria and fungi. In this review, isolation, characterization, functional diversity, transcription regulatory mechanisms and phylogenetic analysis of phytoene dehydrogenase from different organisms are illustrated. This paper will provide insights into phytoene dehydrogenase and may facilitate the optimization of carotenoids production in genetic engineering strategy.