Selection based on genotypes at marker loci may increase the efficiency of plant improvement. Before developing marker-based selection schemes, it is necessary to understand the kinds of relationships that exist between marker loci and genes involved in expression of the desired traits. Two interspecific crosses of soybean, Glycine max (L.) Merr. x G. soja Sieb. & Zucc., were used to examine the relationships between isozyme marker loci an agronomic traits. The parents possessed different alleles at six isozyme loci for Cross 1 (A80-244036 x PI 326581) and eight isozyme loci for Cross 2 (A81-157007 x PI 342618A). Approximately 4000 BC[subscript]2F[subscript]4-derived lines obtained by single seed descent from 10 BC[subscript]2F[subscript]1 plants from each cross were evaluated in two replications at two locations for maturity (MAT), height (HT), lodging (LDG), plant type (PLT), and vining (VNG). Lines were identified that were homozygous for G. soja alleles at different numbers of marker loci, from 0 to 5. Within each locus class there was a number of specific enzyme genotypes, and each enzyme genotype was represented by a number of lines from different BC[subscript]2F[subscript]1 families. Associations were observed for specific enzyme genotypes and every quantitative trait in both crosses, but the particular isozyme genotype/quantitative trait relationships were population specific. The number of homozygous marker loci was associated with differences in HT, LDG, PLT, and VNG, and the trends were similar across populations. Interactions among loci affecting the quantitative traits were observed in the 2-, 3-, 4-, and 5-locus isozyme genotypes.