Aquilegia vulgarisis a widespread ornamental plant. The species is well known for a huge variation of different flower colors and can even be considered as a model species for the evolution of flower morphology. Anthocyanins are a major pigment group responsible for pigmentation of flowers inA. vulgarisand many plant species. Here, we report a highly continuous genome sequence of a EuropeanAquilegia vulgarisplant displaying purple flowers. The corresponding annotation facilitates research on flower color and morphology evolution. Candidate genes for all steps in the core anthocyanidin biosynthesis were identified and investigated with respect to their expression in different seedling parts. The discovery of a flavonoid 3’5’ hydroxylase (F3’5’H), a gene required for the biosynthesis bluish delphinidin derivatives, matches previous reports about metabolites and transcripts inA. vulgaris.