Abstract: Two types of structural variation have been analyzed in 100 well-sequenced flax genomes: gene presence–absence, and gene copy number. Individual flax varieties bear deletions of DNA sequences, insertions of new sequences, and sequence amplification in comparison to the reference genome. The functional annotation of the corresponding regions in the reference genome and new sequences shows that they encode proteins involved in plant response to biotic and abiotic stresses, energy metabolism, viral and transposon activity, and the formation of cell membranes. Our results suggest that these functions are indicative of the adaptation of varieties to regional growing conditions by means of structural variation.