The isoflavones in kudzu roots, especially the C-glycosylated isoflavone puerarin, have been linked to many health benefits. Puerarin contains a carbon-carbon glycosidic bond that can withstand hydrolysis. The C-glycosylation reaction in the biosynthesis of puerarin has not been thoroughly investigated, with conflicting reports suggesting that it could take place on daidzein, isoliquiritigenin, or 2,7,4ʹ-trihydroxyisoflavanone. Kudzu species were identified for use in comparative transcriptomics. A non-puerarin producing kudzu was identified as Pueraria phaseoloides and a puerarin producing kudzu was identified as Pueraria montana lobata. Through the use of the plant secondary product glycosyltransferase (PSPG) motif, glycosyltransferases (UGTs) were identified from the transcriptomes. The UGTs that had higher digital expression in P. m. lobata were examined further using additional tools to home in on the UGT that could be responsible for puerarin biosynthesis. One of the UGTs identified, UGT71T5, had previously been characterized from kudzu as a C-glycosyltransferase involved in puerarin biosynthesis through in vitro enzyme activity (with daidzein) and a gain of function approach in soybean hairy roots. Previous studies have not supported the end-product of a pathway such as daidzein as the target for C-glycosylation, and no genetic analysis of UGT function had been conducted in kudzu. The activity of recombinant UGT71T5 with daidzein was confirmed in the present work. Following the development of a kudzu hairy root system, UGT71T5 expression was then knocked down by RNA interference (RNAi). When compared to control hairy roots there was a large reduction in puerarin content in the UGT71T5-RNAi roots, confirming the role of this enzyme in puerarin biosynthesis. Isotopic labeling of kudzu plants revealed that labeled daidzein could be directly incorporated into puerarin; however, the percent incorporation of daidzein was substantially lower than that of L-phenylalanine, a compound at the start of the pathway to isoflavone synthesis. The knockdown of 2-hydroxisoflavanone synthase (2-HIS) in kudzu hairy roots blocked formation of puerarin and daidzin (7-O-glycosyldaidzein), and was accompanied by accumulation of C-glycosylated isoliquiritigenin and C-glycosylated liquiritigenin. These compounds were found in low amounts in control hairy roots, but were virtually absent in UGT71T5 knockdown hairy roots. The knockdown of 2-hydroxyisoflavanone dehydratase (2-HID) in kudzu hairy roots resulted in a slight reduction in puerarin but no change to daidzin levels, suggesting that C-glycosylation might stabilize the substrate for 2-HID which can otherwise spontaneously dehydrate. Taken together these results reveal that UGT71T5 is likely the major C-glycosyltransferase involved in puerarin biosynthesis in kudzu. They also provide evidence for an alternative pathway to puerarin biosynthesis through the C-glycosylation of isoliquiritigenin or its immediate precursor. In one pathway, UGT71T5 acts as an operationally soluble enzyme that can directly C-glycosylate daidzein, and in the other pathway UGT71T5 acts as part of a metabolic channel for conversion of a C-glycosylated earlier precursor to puerarin. Other UGT enzymes identified in this work did not show C-glycosyltransferase activity; however, three enzymes showed activity in vitro that could be useful for introducing novel regiospecificity in biochemical synthesis of flavonoid glycosides.