The present invention relates to the isolation of a second omega-3 fatty acid desaturase (FAD3) gene in flax (Linum usitatissimum) and its promoter region, as well as the identification of FAD3 mutant alleles, and the development of markers for wild type and mutated alleles. The FAD3 genes encode the enzymes which control omega-3 fatty acid desaturation and, thus, the levels of linolenic acid (18:3(n-3)). Accordingly, the molecules of the present invention can be utilized, for example, to develop markers for the mutations in flax FAD3 genes and for seed-specific modification of fatty acid and protein compositions in plant seeds.