In Canada, flax is an oilseed crop known for its high content of omega-3 (alpha linolenic acid), an essential fatty acid associated with numerous health attributes. In Europe, flax is mostly grown as a fibre crop used in the fabrication of linen and other high quality technical fibre products. Flax’s latin name, Linum usitatissimum, means “most useful” which indeed reflects the usefulness of this dual purpose crop. Flax’s estimated genome size of 373Mb is smaller than rice and makes it a good target for rapid advancement using genomics tools. Here, we developed 1,082 SSR markers from EST and BAC end sequences. Between 389 and 466 SSR markers were mapped on three segregating populations. A consensus SSR map of 774 SSR markers grouped in 15 linkage groups spanning ~2,060 cM was constructed. A Reduced Genome Representation (RGR) combined with a Genotyping by Sequencing (GBS) approach was used to develop SNP-based maps of two segregating populations. The CDC Bethune/Macbeth RIL population was sequenced using Illumina GA-II. A total of 30,814 SNPs were identified and SNPs (4,571) present in >80% of the segregating lines were mapped. The SP2047/UGG5-5 DH population was sequenced using Illumina HiSeq. This mapping data was used to anchor the CDC Bethune physical map. A total of 251 FPC contigs corresponding to 310Mb (~83%) of the estimated genome size of CDC Bethune have been anchored. Mapping and anchoring of the SP2047/UGG5-5 SNP map and construction of the consensus SSR- and SNP-based map will be illustrated.