Fusarium foot and root rot is one of the most important soilborne diseases of cereals, specifically on durum wheat which is the main cultivated species in the Mediterranean regions. This work aimed to evaluate the response of durum wheat and bread wheat to this disease under different climatic conditions. The disease parameters, grain yield loss as well as thousand kernel weight (TKW), heading date and height of plant were evaluated on 29 durum and bread wheat genotypes during two years. Overall, durum wheat grain yield was strongly and negatively correlated with disease parameters, heading date, and positively with plant height and TKW compared to bread wheat. In the drier year, the 24 durum wheat genotypes were more susceptible to the disease than the five bread wheat varieties while some of them showed less disease during the wetter year. Bread wheat maintained the same behavior in both years vs. durum wheat. Grain yield loss was higher on durum wheat compared to bread wheat. It was the same in both years (56 and 51%) for durum wheat and was significantly (p < 0.01) lower in the drier (24%) compared to the wetter year (44%) for bread wheat. This work confirmed the susceptibility of Tunisian durum wheat to the disease compared to bread wheat and calls attention to the potential vulnerability of this important Mediterranean food crop under a hotter, drier climate. More research is needed to investigate adaptation to drought and plant defense mechanisms and to breed for resistance to this disease.