Glycine soja Sieb. & Zucc. is the wild progenitor of the cultivated soybean, Glycine max (L.) Merr. Although G. soja is agronomically undesirable, it is a potential source of new germplasm for breeding programs. Marker loci may be useful in an introgression program to enhance the recovery of desirable traits of the cultivated species by decreasing the number of segregants that must be evaluated in the field. Isozyme loci have a number of characteristics that make them desirable as markers. Before developing marker-based selection schemes, it is necessary to understand the relationships that exist between isozyme loci and genes involved in the expression of the desired traits. Two crosses between G. max and G. soja parents were used to study the association between isozyme marker loci and quantitative traits. The parents possessed different alleles at six isozyme loci for Cross 1 (A80-244036 x PI 326581) and at eight isozyme loci for Cross 2 (A81-157007 x PI 342618A). A total of 480 lines from the two crosses were evaluated in two replications at two locations for time of maturity (MAT), lodging, plant height, vining, plant type, seed yield, content of seed protein, oil, palmitic acid, stearic acid, oleic acid, linoleic acid, and linolenic acid. Lines were grouped in locus classes, from 0 to 5, according to the number of loci homozygous for the G. soja alleles they possessed. Within each locus class, there were a number of isozyme genotypes, each represented by five random lines. Associations were found between quantitative traits and locus classes, however, the relationships were specific for each population. Associations observed between the quantitative traits and particular isozyme genotypes also were found to be population specific in most cases. A relationship between isozyme phosphoglucomutase (locus Pgm1) and maturity was consistent over populations.