The uridine diphosphate glycosyltransferase (UGT) plays the central role in glycosylation of small molecules by transferring sugars to various acceptors including bioactive natural products in plants. UGT89C1 from Arabidopsis thaliana is a novel UGT, a rhamnosyltransferase, specifically recognizes UDP-L-rhamnose as donor. To provide an insight into the sugar specificity for UDP-L-rhamnose and interactions between UGT89C1 and its substrates, the UGT89C1 was expressed in Escherichia coli and purified toward biochemical and structural studies. Enzyme activity assay was performed, and the recombinant UGT89C1 recognized UDP-L-rhamnose and rhamnosylated kaempferol. Crystals of AtUGT89C1 were obtained, they diffracted to 2.7 angstrom resolution and belonged to space group I4(1). AtUGT89C1 was also co-crystallized with UDP. Interestingly, two crystal forms were obtained in the same crystallization condition, including the previous I4(1) crystal form, and the new crystal form that diffracted to 3.0 angstrom resolution and belonged to space group P2(1).