The intensity of flower colour, mainly determined by the amount of anthocyanin, is an important horticultural trait. To modulate flower colour intensity, post-transcriptional gene silencing (PTGS)-based technology has been widely used. The constraint of PTGS, however, is that it requires a high degree of conservation in the nucleotide sequences of the target and the silencer. Further, it is difficult to restrict PTGS to the desired tissue or organ due to its systemic spread. To overcome these problems, dominant-negative chalcone synthase (CHS) enzymes have been developed by mutating a cysteine that is essential for the catalytic activity and a methionine that protrudes into the adjoining CHS monomer, as shown through crystallography. The dominant-negative action of mutated CHS enzymes from Mazus japonicus are demonstrated using transgenic Arabidopsis. Also, the modulation of Petunia flower colour intensity by the dominant-negative CHS is shown. The data support the crystallography result showing the importance of the protruding methionine for the function of the adjoining CHS monomer. Furthermore, the modulation of anthocyanin production by the mutated Mazus CHS in Arabidopsis and petunia suggests that the dominant-negative CHS can be used even in distantly related species.