Incidence of natural light stress renders it important to enhance our understanding of the mechanisms by which plants protect themselves from harmful effects of UV-B irradiation, as this is critical for fitness of land plant species. Here we describe natural variation of a class of phenylacylated-flavonols (saiginols), which accumulate to high levels in floral tissues of Arabidopsis. They were identified in a subset of accessions, especially those deriving from latitudes between 16° and 43° North. Investigation of introgression line populations using metabolic and transcript profiling, combined with genomic sequence analysis, allowed the identification of flavonol-phenylacyltransferase 2 (FPT2) that is responsible for the production of saiginols and conferring greater UV light tolerance in planta. Furthermore, analysis of polymorphism within the FPT duplicated region provides an evolutionary framework of the natural history of this locus in the Brassicaceae.