Early maturity is an important objective for breeding flax adapted to the Western Canada. Crop canopy traits influence seed yield; however, studying its effects is challenging due to the complexity and limited knowledge of the genetics of this trait. The objectives of this research are : i) to characterize flax accessions from the Canadian gene bank collection for early flowering, maturity and canopy traits; ii) to identify SSR markers associated with plant branching and leaf area index (LAI); iii) to use Structural Equation Modeling (SEM) to identify canopy variables with significant effects on yield. The flax core collection, consisting of approximately 381 accessions, was grown at the Kernen Crop Research Farm in 2010 and 2011. Additionally, 17 early and 17 late flowering accessions from the flax core collection were screened and their phenotypic responses in both growth chamber and field environments were measured. A large amount of phenotypic diversity was observed in long day and short day environments in these experiments. Some accessions appeared to be more photosensitive, while others were photoperiod insensitive. The genetic control of canopy traits such as LAI and plant branching were studied using association mapping. Genotyping of the core collection was conducted using 375 SSR markers. Population structure analysis assigned the 381 flax accessions in the core collection into four distinct groups. Model comparison revealed that the mixed linear model reduced spurious marker trait associations. A total of 26 markers were identified to be significantly associated with plant branching and LAI. The simultaneous examination of crop phenology and canopy traits to seed yield was performed using SEM analysis. The results indicated greater plant stand resulted in higher irradiance absorption and which resulted in greater seed yield. Days to flowering had a significant negative effect on seed yield and growing degree days to maturity had a significant effect on seed yield. Plant branching and plant height had a positive non-linear effect on seed yield. This study has provided several insights into molecular approaches and statistical methods to improve flax breeding.