Linseed oil rich in omega-3 fatty acid is being used as a plant based functional food and as a raw material for environment-friendly products such as linoleum. Stem fibres from flax have multiple end uses in industry. To accelerate flax improvement by genomics assisted breeding, a project entitled Total Utilization Flax GENomics (<u>www.tufgen.ca</u>) was initiated in 2009. Here, we report the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES) from a total of 43,776 BAC clones from the cultivar CDC Bethune. High stringency assembly of 32,025 high quality fingerprints resulted in 416 contigs, spanning ~368 Mb, covering ~99.4% of the revised estimated genome size (370 Mb). The N50 size of the contigs was estimated at 1,494 kb with the longest contig spanning 5,562 kb, indicating the robust quality of the physical map. Generation of ~54.6 Mb sequence, covering 14.8% of the genome from 80,337 BES and homology based annotation revealed the uniqueness of the flax genome compared to other plant genomes: 1. the proportion of ribosomal DNA was found to be very high (~13.8%) and; 2. the contribution of known transposable elements was low (~6.1%), whereas, novel repetitive fractions occupy ~7.4% of the genome. Comparative analysis against NCBI-ESTs and flax-ESTs revealed that ~5.6% of the flax transcriptome is unique. Integration of the physical contigs and BES with a dense linkage map being developed in our lab provides a valuable modern tool for map based cloning of genes controlling important traits, as well as improving the accuracy of the whole-genome shotgun assembly being generated under the TUFGEN consortium.