DNA probes from the L6 rust resistance gene of flax (Linum usitatissimum) hybridize to resistance genes at the unlinked M locus, indicating sequence similarities between genes at the two loci. Genetic and molecular data indicate that the L locus is simple and contains a single gene with 13 alleles and that the M locus is complex and contains a tandem array of genes of similar sequence. Thus the evolution of these two related loci has been different. The consequence of the contrasting structures of the L and M loci on the evolution of different rust resistance specificities can now be investigated at the molecular level