Durum (2n=4x=28; AABB) wheat is the grain of choice for the production of high-quality pasta products. Fusarium spp. are causal pathogens for Fusarium Head Blight (FHB). Limited host resistance to this disease exists among adapated durum cultivars. The use of Tunisian-derived durum lines for integration of FHB resistance in cultivars was evaluated. The genetic characterization of FHB resistance was evaluated, and markers assosciated with FHB resistance are presented in two populations. Two backcross inbred line (BIL) populations derived from cross between a resistant durum genotype `Tunisian 108' and susceptible durum wheat cultivars `Ben' and `Lebsock' were screened to identify QTL for FHB resistance. Analysis of variance showed significant effect of genotypes on FHB severity and incidence despite high level of interaction between environment and genotypes. A total of 329 and 331 DArT and microsatellite markers covered a distance of 1887.6 and 1748 cM in two populations respectively. Composite interval mapping using two linkage maps and the phenotypic data revealed 11 different FHB resistance QTL on seven different chromosomes (1A, 1B, 2B, 3B, 5A, 5B, and 7B) in Tunisian/Ben derived population and 15 different FHB resistant QTL on seven different chromosomes (1A, 1B, 3A, 3B, 4A, 5A, and 6B) in population derived from cross between Tunisian/Lebsock. At least two novel QTL were identified on chromosome 2B (Qfhb.ndsu-2B) 4A (Qfhs.ndsu-4A) in Tunisian/Ben//Ben and Tunisian/Lebsock//Lebsock population respectively. Location of the two FHB resistance QTL on chromosome 1B and two QTL on 5A were identical in both populations. Owing to cumulative effects of resistance QTL, high level of transgressive segregation was observed in both populations. Our finding revealed an alternative tetraploid FHB resistance source from Tunisian genomic background that can be utilized with associated markers for wheat geremplasm enhancement.