Durum wheat is an economically important crop for western Canadian farmers. Fusarium head blight (FHB) is one of the most destructive diseases that threatens durum production in western Canada. FHB reduces yield and end-use quality and contaminates the grain with fungal mycotoxins, most commonly deoxynivalenol also known as DON. Serious outbreaks of FHB frequently occur in durum wheat in Western Canada, and combining genetic resistance with fungicide application is a cost effective approach to control this disease. However, there is limited variation of genetic resistance to FHB in elite Canadian durum cultivars. To explore and identify useful genetic variation of FHB resistance for the improvement of Canadian durum wheat, we assembled an association mapping (AM) panel of diverse durum germplasm and performed genome-wide association analysis. The population was evaluated for FHB incidence and severity over three years in three nursery sites. The incidence, severity and index followed continuous distributions that showed a preponderance of susceptible lines. With SNP markers identified from the 90K SNP infimum array, a genome wide association study (GWAS) was performed. Genomic loci associated with FHB resistance were found on almost all 14 chromosomes. QTL on 2A, 3A, 4A, 6A, 1B, 3B and 4B produced large and stable effects on FHB resistance. The SNP based KASP markers spanning these genomic regions were developed for validation in breeding. Loci affecting flowering time on chromosomes 1B, 3B and 4A and plant height on 6A overlapped with loci for FHB resistance on chromosomes 1B, 3B, 4A and 6A. These findings reinforce the need to stratify by phenology and height experimental lines in nurseries to differentiate the pleiotropic or linkage effects of genes for FHB resistance and plant height and flowering time from disease escape.