AbstractSoybean [Glycine max (L.) Merr.] oil from current commercial cultivars typically contains ca. 8% linolenic acid. Inheritance studies have shown that linolenic acid concentration in soybean seed is determined by at least two genes which govern activity of the predominant ω‐6 and ω‐3 desaturases. Selection of germplasm exhibiting homozygous recessive alleles that encode these desaturases has enabled development of soybeans having less than 3.0% linolenic acid. However, accessions of the wild ancestor of modern soybean cultivars, Glycine soja (Sieb. and Zucc.), have oils containing twice the highest linolenic acid concentration found in normal G. max cultivars. Although little is known about inheritance of linolenic acid in wild soybean, it would appear that additional or alternative forms of genes may govern its synthesis. To test this hypothesis, cultivated soybean germplasm was hybridized with wild soybean genotypes having significant differences in linolenic acid concentration. Seed of F3 progeny from these G. max x G. soja populations exhibited distinct segregation patterns for relative estimates of ω‐6 and ω‐3 desaturase activity. Frequency class distribution analyses of the segregation patterns, and linear relations between median ω‐6 or ω‐3 desaturation estimates and corresponding linolenic acid concentration among allelic classes from these populations suggested the high‐linolenic acid trait in wild soybean genotypes was determined by a set of desaturase alleles that were different from corresponding alleles in G. max. Introgression of these alternative alleles in G. max germplasm opens a new avenue of research on the genitic regulation of linolenic acid, and may lead to the production of highly polyunsaturated soybean oils for various industrial applications.