Lectin protein and Kunitz trypsin inhibitor (KTI) protein of mature soybean seed are a main antinutritional factor in soybean seed. The Le gene controls a lectin protein and Ti gene controls the KTI protein in soybean. Ti locus has been located on linkage group 9 in the classical linkage map of soybean. Position of Le locus on linkage map was not identified. Genetic relationship between Ti locus and Le locus could be useful in soybean breeding program for the genetic elimination of these factors. The objective of this study was to determine the independent inheritance or linkage between Ti locus and Le locus in soybean seed. Two F2 populations were developed from three parents (Gaechuck#1, T102, and PI548415). The F1 seeds from Gaechuck#1 (titiLeLe) x T102 (TiTilele) and Gaechuck#1 (titiLeLe) x PI548415 (TiTilele) were obtained. The lectin and KTI protein were analysed from F2 seeds harvested from the F1 plants to find independent assortment or linkage between Ti locus and Le locus. The segregation ratios of 3 : 1 for Le locus (129 Le_ : 44 lele) and Ti locus (132 Ti_ : 41 titi) and were observed. The segregation ratios of 9 : 3 : 3 : 1 (95 Le_Li_ : 34 Le_titi: 37 leleTi_ : 7 leletiti) between Le gene and Ti gene in F2 seeds were observed. This data showed that Ti gene was inherited independently with the Le gene in soybean. These results will be helpful in breeding program for selecting the line with lacking both KTI and lectin protein in soybean.