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In the present investigation, two soybean genotypes with 35.43% and 44.40% protein content were evaluated for glycinin (7S), β-conglycinin (11S), and also assessed for anti-nutritional factors like kunitz trypsin inhibitor (KTI), off-flavourgenerating lipoxygenase, in vitro protein digestibility (IVPD), and amino acid composition. Concentration of α’, α and β subunit of β-conglycinin (7S) and the acidic subunit of glycinin (11S) was significantly (P<0.05) less, while the basic subunit was higher in low-protein genotype compared to the high-protein genotype. However, no significant difference was noted for the ratio of 11S to 7S fraction. KTI was significantly (P<0.05) less in low-protein genotype (LPN7N101), though no significant difference was noted between low- and high-protein soybean genotype (EC 468447) for lipoxygenase. IVPD of low-protein genotype was significantly (P<0.05) higher than the high protein genotype. Concentration of arginine (4.27%), phenylalanine (2.69%), valine (2.02%), glutamate (8.98%), aspartate (4.83%), and glycine (2.11%) in high-protein genotype was significantly (P<0.05) higher than the corresponding values (2.81, 1.81, 1.48, 4.99, 3.13 and 1.47%, respectively) of these amino acids in low-protein genotype.