Soybean [Glycine max (L.) Merr.] genotypes have been developed with increased β-conglycinin (BC) and reduced glycinin to improve the quality and health benefits of food products containing soybean protein. The changes in protein composition are due to the five recessive alleles, gy1, gy2, gy3, gy4, and gy5, that modify glycinin concentration. The objective of this study was to evaluate the influence of the gy alleles on protein composition and agronomic traits. Nineteen lines in each of eight genotypic classes involving different combinations of gy alleles from five populations were evaluated for protein composition, seed yield, and maturity in 2008.The BC concentration of lines was maximized with the gy1,2, gy4, and gy5 alleles, but the gy3 allele also was required to obtain 0 g kg−1 of glycinin. The effect of the recessive alleles on the increase in BC concentration was greatest for gy1,2 (98 g kg−1), intermediate for gy5 (44 g kg−1), and least for gy3 (18 g kg−1). There were significant differences in mean protein and oil concentration, grain yield, and maturity among the eight genotypic classes; however, the differences were not consistent among the populations. It should be possible to develop soybean cultivars with increased BC and decreased glycinin concentration that have protein and oil concentration, grain yield, and maturity similar to cultivars with normal protein composition.