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C-glycosides are an important class of bioactive natural products, and the C-glycosidic bonds are usually catalyzed by C-glycosyltransferases. In this work, an efficient and rare CGT, LaCGT1, was discovered from the aquatic plant Lemna aequinoctialis. LaCGT1 could accept five sugar donors (UDP-Glc/-Xyl/-Gal/-GlcNAc/-Ara) to catalyze C-glycosylation, and showed strong preference to uridine 5′-diphosphate xylose (UDP-Xyl). LaCGT1 catalyzed at least six substrates using UDP-Xyl as sugar donor, with conversion rates of > 95%. Three xylosides were obtained by scaled-up enzymatic catalysis, and their structures were identified by 1D NMR, 2D NMR, and HR-ESIMS data analyses. Molecular modeling and site-directed mutagenesis indicated that R271, W357, D378, and Q379 residues were key amino acids contributing to sugar donor recognition of UDP-Xyl. LaCGT1 could be a promising catalyst to prepare bioactive flavonoid C-xylosides.