Photosynthetic organisms require light but also rely on photoprotection to preempt photodamage induced by excess light. The xanthophyll cycle, a light-dependent carotenoid interconversion, plays a key role in the on- and offset of Non-Photochemical Quenching (NPQ), a form of excess energy dissipation through heat. While in most photosynthetic eukaryotes, including brown algae, green algae and plants, the violaxanthin cycle is prevalent, haptophytes and diatoms rely on the diadinoxanthin cycle to regulate NPQ. Diatoms also contain small amounts of violaxanthin cycle pigments, thought to serve only as precursors in xanthophylls biosynthesis. Both cycles are catalyzed by the enzymes violaxanthin de-epoxidase (VDE) and zeaxanthin epoxidase (ZEP). Here, we characterized the role of VDE and different ZEP encoding paralogs (ZEP2andZEP3) in the model diatomPhaeodactylum tricornutum. We generated the respective knockout lines and treated exponentially growing mutants and wild type with periodic high light stress. We conclude that VDE and ZEP3 are the main regulators of the diadinoxanthin cycle. Under the same conditions,ZEP2knockouts accumulated mainly pigments of the violaxanthin cycle instead of the diadinoxanthin cycle. Intriguingly, violaxanthin cycle pigments contributed to the generation of NPQ with the same quenching efficiency of diadinoxanthin cycle pigments, demonstrating that both major xanthophyll cycles present in nature can provide NPQ in the same organism, with similar properties. Consequently, the prevalence of the diadinoxanthin cycle in diatoms has not been driven by its higher quenching efficiency but likely resulted from the selective advantage of a faster switch between photoprotection and light harvesting.Significance StatementDiatoms have a key role in almost any aquatic habitat, participate in nutrient cycling and contribute as much as the most productive terrestrial ecosystems to the global primary productivity. Diatoms are also regarded as biological factories of high value bioactive compounds, like carotenoids. Here, we investigated one of the most significant photoprotection mechanisms, the xanthophyll cycle, which relies on carotenoids to dissipate detrimental excess of light energy. Although diatoms use the so-called diadinoxanthin cycle, we discovered that the ancestral violaxanthin cycle, ubiquitous in plants and algae, can also contribute to photoprotection in these algae. We demonstrate that both cycles can function synergistically and with comparable efficiency within the same species, offering a new perspective on the evolution of xanthophyll-mediated photoprotection.