“Cinerarin” is a polyacylated anthocyanin that is responsible for the blue coloration of cineraria (Senecio cruentus) flowers. We isolated a full-length cDNA (Sc3MaT) encoding a putative anthocyanin acyltransferase from S. cruentus. The Sc3MaT cDNA was expressed in Escherichia coli cells and the expression product was purified to homogeneity and functionally characterized. The Sc3MaT could catalyze the regiospecific malonyl transfer from malonyl-CoA (K_m, 61μM) to pelargonidin 3-O-glucoside (K_m, 11μM) to produce pelargonidin 3-O-6”-O-malonylglucoside with a k_cat value of 8.8 s^-1. The specificities for acyl donors and acceptors were highly restricted to malonyl-CoA and anthocyanidin 3-O-glucoside, respectively. Therefore, it may be concluded that Sc3MaT is a malonyl-CoA:anthocyanidin 3-O-glucoside-6”-O-malonyltransferase. The other enzymatic properties of Sc3MaT were comparable with those of known anthocyanin acyltransferases. Because a reaction product of Sc3MaT, delphinidin 3-O-6”-O-malonyglucoside, constitutes a part of cinerarin, Sc3MaT is probably involved in the cinerarin biosynthesis in this plant.