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The vulnerable plant Dalbergia tonkinensis Prain is a rare species in Vietnam. In the course of our studies on biologically active plants, we performed serine protease enzyme screenings. The results suggest that at concentrations of 25-250 ng/mL, methanol extracts of leaf and root, root ethanol extract and its dichloromethane fraction, and heartwood water decoction extract can serve as useful sources to stimulate trypsin enzyme activity. In addition, water decoction extracts of leaf and stem bark may explain unknown ethno-pharmacology due to the high inhibitory effects in enzyme assays using trypsin, chymotrypsin, and elastase. Among 23 isolated compounds and two semi-synthetic derivatives tested, quercetin (17) inhibits the activities of trypsin and chymotrypsin with IC 50 9.7 µM. Flavonoids categorized as flavanone, isoflavanone, flavone, isoflavone, pretocarpan, aurone, and neoflavanone demonstrated variable activities. Several substitutions are closely correlated with protease actions, including hydroxylation at C-3 and C-3' in flavone and C-5 and C-3' in isoflavone, hydroxylation at C-3, C-5 and C-3', carboxylation at C-6 and C-8, and 7-substitution in flavanone; 7-substitution and methoxylation at C-3' in isoflavanone; and lactone ring opening in neoflavanone. In the assessment of casein cleavage, at a dose of 25 ng/mL, leaf water decoction extract demonstrates an inhibitory effect on casein cleavage by trypsin, whereas ethanol and methanol extracts of the root caused activation.