The major anthocyanin in A. thaliana is a cyanidin derivative modified by glycosylation as well as by the addition of three acyl moieties: malonyl, p-coumaroyl, and sinapoyl. We have isolated a member of the BAHD acyltransferase family which catalyzes this malonylation reaction by combining a reverse genetics approach with biochemical genomics. A mutant line containing a T-DNA insertion in At3g29590, the gene encoding the malonylating enzyme, is incapable of producing malonylated anthocyanins. Transgenic plants harboring an RNAi silencing cassette for At3g29590 demonstrate a positive correlation between reduction in the At3g29590 gene transcript and the decrease of malonylated anthocyanins. Transcript levels for both At3g29590 and the epistatic gene At4g14090, encoding 5-O-anthocyanin glucosyltransferase, increase in several plant lines as they accumulate anthocyanin pigments. Investigation of the heterologously expressed and purified malonylating enzyme showed that the activity is specific for malonyl-CoA and for anthocyanins with 5-O-glucosylation. The malonyl transfer itself occurs only to the 5-O-glucoside function, and not to any of the other sugar moieties present in A. thaliana anthocyanins. Hence, both in vivo and in vitro results define the activity of the At3g29590-encoded enzyme as an anthocyanin 5-O-glucoside-6''-O-malonyltransferase (At5MAT).