Ornamental gentian plants have vivid-blue flowers. The main factor contributing to the flower colour is the accumulation of a polyacylated delphinidin ‘gentiodelphin’ in their petals. Although in vitro studies proposed that acylation plays an important role in the stability and development of gentian blue colour, the in vivo stability of the polyacylated anthocyanin was not clearly demonstrated. Thus, to reveal the importance of anthocyanin modification, especially acylation, and to engineer new colours of gentian flowers, we used chimeric RNAi technology to produce transgenic gentian plants with downregulated anthocyanin 5,3′-aromatic acyltransferase (5/3′AT) and flavonoid 3′,5′-hydroxylase (F3′5′H) activities, which are both essential enzymes for gentiodelphin biosynthesis. Two lines of flower colour-modified plants were obtained from fifteen transgenic gentian plants. Clone no. 1 exhibited a lilac flower colour and clone no. 15 exhibited pale-blue flowers. RNA gel blot analysis confirmed that both transgenic lines had markedly suppressed 5/3′AT transcripts, whereas clone no. 15 had fewer F3′5′H transcripts than clone no. 1 and untransformed control plants. HPLC analysis of anthocyanin compositions showed that downregulation of the 5/3′AT gene led to increased accumulation of non-acylated anthocyanins, as expected. These results demonstrated that genetic engineering to reduce the accumulation of polyacylated anthocyanins could cause modulations of flower colour