Many patients with diabetes use self-measurement devices for blood glucose to understand their blood glucose levels. Most of these devices use FAD-dependent glucose dehydrogenase (FAD-GDH) to determine blood glucose levels. For this purpose, FAD-GDHs specifically oxidizing glucose among the sugars present in blood are required. Many FAD-GDHs with high substrate specificity have been reported previously; however, their substrate specificity is insufficient as they also react with xylose. Therefore, we aimed to identify FAD-GDHs without xylose reactivity. We screened and obtained a new enzyme from Colletotrichum plurivorum (CpGDH). CpGDH showed high activity to glucose in the presence of electron mediators but low activity to xylose. We prepared the glucose oxidation products using CpGDH and subjected to TLC, HPLC, mass spectrometry, and NMR analyses. The results demonstrated that CpGDH is a previously unknown FAD-dependent glucose 6-dehydrogenase (FAD-G6DH) that oxidizes glucose to glucuronic acid. The stoichiometric ratio of the substrate and electron mediator was 1:2, suggesting that CpGDH catalyzes two-step oxidation reactions, including oxidation of primary alcohols to aldehydes and of aldehydes to carboxylic acids. We concluded that CpGDH has the unique substrate-binding manner based on the result of docking simulation of CpGDH with a substrate glucose. We then constructed a phylogenetic tree of carbohydrate-related flavoproteins including FAD-G6DHs, indicating that FAD-G6DHs are different from the known FAD-dependent oxidoreductases. Overall, this study is the first to report FAD-G6DHs. These results will likely contribute to the development of more accurate blood glucose sensors and further research on the metabolisms of glucosides and their metabolites.