Aegilops tauschii, the D genome donor of wheat, is an invaluable source of genetic variability, which can be utilized for broadening the wheat gene pool. Linked leaf rust resistance and non-glaucousness genes transferred from Ae. tauschii to cultivated wheat variety WH542 were mapped in the present study. Genetic analysis in an F2 population from a BC3 plant derived from the cross Triticum durum cv. PBW114/Ae. tauschii acc. pau14195//4*T. aestivum cv. WH542 revealed monogenic dominant inheritance for both the traits. The leaf rust resistance and the non-glaucousness gene were tentatively named LrT and IwT, respectively. Leaf rust resistance gene exhibited all stage resistance. SSR markers Xbarc124, Xgdm5, Xgdm35, Xcfd51 and EST-derived markers Xcau96 and Xte6 on chromosome 2DS were linked with both genes. Chromosomal assignments of the genes were confirmed by testing linked SSR markers on Chinese Spring nulli-tetrasomics lines. SSR markers Xcau96 (1.6 cM) and Xbarc124 (0.6 cM) flanked LrT and Xgdm35 (4.1 cM) and Xte6 (2.5 cM) flanked non-glaucousness gene. LrT and IwT showed a recombination distance of 3.4 cM. Hence, IwT can be used as an easy to score morphological marker of LrT during its transfer to other glaucous backgrounds.