Salinity affects durum wheat [Triticum turgidum L. ssp. durum (Desf.)] more than it affects bread wheat (Triticum aestivum L.), and results in lower yield for durum wheat cultivars grown on salt-affected soils. A novel source of salt tolerance in the form of a sodium exclusion trait, identified previously in a screen of tetraploid wheat germplasm, was mapped using a QTL approach. The trait, measured as low Na+ concentration in the leaf blade, was mapped on a population derived from a cross between the low Na+ landrace and the cultivar Tamaroi. The use of AFLP, RFLP and microsatellite markers identified a locus, named Nax1 (Na exclusion), on chromosome 2AL, which accounted for approximately 38% of the phenotypic variation in the mapping population. Markers linked to the Nax1 locus also associated closely with low Na+ progeny in a genetically unrelated population. A microsatellite marker closely linked to the Nax1 locus was validated in genetically diverse backgrounds, and proven to be useful for marker-assisted selection in a durum wheat breeding program.