Flax is often considered a total utilization crop because of the potential to extract value from two distinct products - seeds and stem fibres. However, very little genetic information is available on flax fibre genetics in comparison to oil improvement studies. In order to gain a detailed understanding of genetic control of the fibre concentration and search for the possibilities of developing dual purpose flax lines using both seed oil and stem fibre, the following studies were initiated: The first study evaluated the fibre and oil-related traits in a recombinant inbred population derived from a cross between a fibre flax variety Viking and an oilseed flax genotype E1747 over multiple locations under western Canadian field conditions. The study confirmed the presence of a significant genotype by environment interaction (p < 0.01) for fibre concentration indicating selection for this trait will be challenging. However, a lack of significant correlation between fibre and oilseed characteristics in field trials was encouraging and strengthened the hypothesis that breeding dual purpose flax types for western Canada is possible. The study also identified potential recombinant inbred lines (RILs) with enhanced fibre concentration as well as oil characteristics for use in future breeding endeavors. The second study established an anatomical basis for further research into flax fibre improvement by studying differences between the stem anatomy of 14 diverse flax genotypes in the field and under controlled environments such as a growth chamber. The results from the study supported the use of controlled environments for the purpose of quick screening of high fibre containing genotypes, especially at the green capsule stage of plant growth. The results also indicated that it was possible to select high fibre oilseed flax lines based on anatomical markers such as average area of single fibre cells, total fibre area and fibre to stem area ratio. In the third study, 17 simple sequence repeat (SSR) and 2 cleaved amplified polymorphic sequences (CAPS) molecular markers were used to assess the extent of genetic variability in the Viking × E1747 RIL population. CAPS markers LuFAD3A and LuFAD3B had the highest marker trait association (p < 0.0001) with linoleic and linolenic acid concentration. SSR markers such as CV8824, 5B6 and LU32 were found to be associated with plant height, oil concentration and protein concentration respectively using single marker analysis and step wise regression analysis. The molecular study confirmed the importance of Viking × E1747 mapping population in identifying genes/ markers related to both fibre and oilseed related traits in flax. In the fourth study, global transcript profiling using cDNA - based microarrays was performed to identify differentially expressed fibre related transcripts between Viking and E1747. The largest group of transcripts (7 %) found more abundant in Viking relative to E1747 fell under the functional group of cell wall development using gene ontology (GO) analysis. Transcripts such as callose synthases, expansins, cytochrome P450, fasciclin-like arabino galactan proteins and β-galactosidases were highly abundant in Viking relative to E1747. The transcripts more abundant in E1747 relative to Viking were UDP – glucose glucosyltransferase, auxin repressed protein, ubiquitin conjugating enzyme, peroxidases and lipid transfer proteins. Quantitative real time PCR results confirmed the suitability of the microarray platform to accurately discriminate transcript profiles between the two diverse flax types. In conclusion, this research has provided a number of new insights into flax fibre genetics. This information lays the foundation for further genetic studies on flax bast fibres and will complement research on developing dual purpose flax varieties.