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β-glucosidase is one of the critical enzymes to the type 2 diabetes, which belongs to a large family of glycoside hydrolases. In this article, we attempted to explore the binding modes between two drugs and β-glucosidases by comparing their bonding modes with β-glucosidases from different species. Results showed that the binding orientations and geometrical conformation of synthetic drug (miglitol) and natural product (quercetin) were all different in all active sites, which may be related to the flexibility of the molecules. Compared with the conformations obtained by density functional theory calculations at the B3LYP/6-31G* level, the docking conformations indicated that the -CH2CH2OH group of miglitol and the B ring of quercetin were the most critical groups to the stabilities in the active sites. Finally, protein sequence alignment was performed under default parameters. Although the sequence similarity is not very high between these β-glucosidases, the residues related to the active sites were conservative; especially the one involved in H-bond interactions between three species, namely soil metagenome, Micrococcus antarcticus and termite Neotermes koshunensis.