Lipoxygenase is responsible for the beany flavor and soybean kunitz trypsin inhibitor protein is responsible for the inferior nutritional quality of unheated or incompletely heated soybean meal. Anthocyanins from black soybean seed coat are known to have many pharmaceutical effect. The object of this study is to select black soybean genotype with absence of lipoxygenase-2,3 (Lx1Lx1lx2lx2lx3lx3) and small seed size. Two cultivars (“Seomoktae” and "Gaechuck#1") were used. "Seomoktae" cultivar has the traits of small seed size, black seed coat, green cotyledon and lipoxygenase protein. "Gaechuck#1" has the traits of big seed size, black seed coat, green cotyledon and lipoxygenase free protein. In the F2 population, the several plants with small seed size and lipoxygenase free protein were selected. In F3 and F4 generation, seed size and lipoxygenase protein was comfirmed from the bulked seed harvested at field. The F5 seeds with small seed size and Lx1Lx1lx2llx2lx3lx3 genotype were planted in the field. Several agronomic traits were evaluated. The lines with appropriate agronomic traits were selected.