Soybean (Glycine max L. Merr.) lines lacking seed lipoxigenases 2 and 3 and with high yield potential were developed at the Grain and Seed Research Center of the University of Costa Rica. Those lines were obtained by crossing selected F3 plants from ‘Kanto-101’ X ‘IAC-8’ with F2 plants selected from ‘Padre’ X ‘Duocrop’. Kanto-101 is a Japanese variety that was used as a donor of lox2 and lox3 genes that inhibit the synthesis of lipoxigenases 2 and 3 in the soybean seed. Elimination of lipoxigenases 2 and 3 considerably improves the taste and odor of the soybean milk. Cultivar Padre was used as a donor of delayed flowering under short day conditions. F11 lines CIGRAS-34, 47, 51 and 57 (lox2,lox3), derived from the double cross, showed an outstanding agronomic performance when compared with high yielding cultivars CIGRAS-06 and 10 (Lox), in three sites. The use of Padre cultivar, carrier of the genes that delay flowering under short day conditions, in tropical soybean breeding programs, is important to develop late maturing lines with good adaptation in tropical regions. Lipoxigenase-free seed of soybeans reach a higher price in the international market and might be a potential export crop to those countries where soybeans are an important component of the human diet.