Summary Genetic engineering of flower color provides biotechnological products such as blue carnations or roses by accumulating delphinidin‐based anthocyanins not naturally existing in these plant species. Betalains are another class of pigments that in plants are only synthesized in the order Caryophyllales. Although they have been engineered in several plant species, especially red‐violet betacyanins, the yellow betaxanthins have yet to be engineered in ornamental plants. We attempted to produce yellow‐flowered gentians by genetic engineering of betaxanthin pigments. First, white‐flowered gentian lines were produced by knocking out the dihydroflavonol 4‐reductase (DFR) gene using CRISPR/Cas9‐mediated genome editing. Beta vulgaris BvCYP76AD6 and Mirabilis jalapa MjDOD, driven by gentian petal‐specific promoters, flavonoid 3′,5′‐hydroxylase (F3′5′H) and anthocyanin 5,3′‐aromatic acyltransferase (AT), respectively, were transformed into the above DFR‐knockout white‐flowered line; the resultant gentian plants had vivid yellow flowers. Expression analysis and pigment analysis revealed petal‐specific expression and accumulation of seven known betaxanthins in their petals to c. 0.06–0.08 μmol g FW−1. Genetic engineering of vivid yellow‐flowered plants can be achieved by combining genome editing and a suitable expression of betaxanthin‐biosynthetic genes in ornamental plants.