Two crosses between Glycine max (L.) Merr. and G. soja Sieb. & Zucc. parents were used to study the association between isozyme marker loci and agronomic and seed composition traits in soybean. The parents possessed different alleles at six isozyme loci for Cross 1 (A80-244036 × PI 326581) and at eight isozyme loci for Cross 2 (A81-157007 × PI 342618A). A total of 480 BC2F4:6 lines from the two crosses was evaluated for 13 traits in two environments. Lines were grouped in locus classes from 0 to 5 according to the number of loci homozygous for the G. soja alleles that they possessed. Within each locus class, each isozyme genotype was represented by five random lines.