The L6 and M rust-resistance genes, representing two of the five rust-resistance gene loci in flax (Linum usitatissimum), have been cloned. The molecular data are fully consistent with earlier genetic data: the L locus is a single gene with multiple alleles expressing different rust resistance specificities, and the M locus is complex, containing an array of about 15 similar genes. Thus, while L6 and M resistance genes have 86% nucleotide identity, their locus structure is very different. These genes encode products belonging to the nucleotide binding site-leucine-rich repeat class of disease-resistance proteins. Analysis of alleles from the L locus and chimeric genes is providing evidence suggesting that important specificity determinants occur in the C-terminal half of the proteins, the region containing the leucine-rich repeats. The isolation and characterization of the rust (Melampsora lini) avirulence genes that correspond to the cloned rust-resistance genes is one of the major challenges remaining to the understanding of this system.