Introgression lines (ILs) were produced from crosses of common hexaploid bread wheat (Triticum aestivum L.) (AABBDD) cultivars with tetraploid durum wheat (Triticum turgidum) (AABB). These ILs were checked against diversity of crop-damaging fungal diseases and especially for leaf and stripe rusts, proved to be the most damaging biotic enemies in the world and especially in South Asia and the southern region of Pakistan. Microsatellite markers (STRs) were used to determine the frequency of translocations found on different chromosomes during the localization of durum wheat (Triticum turgidum). Two independent loci for stripe and leaf rust resistance were found on 2B and 5A during the molecular mapping. The major locus that accounts for 70% of quantitative or phenotypic variance of the trait present on the 5AS-5AL translocated chromosome was closely linked to STR markers Xwmc24, Xgwm95, Xwmc327, Xgwm644, Xgwm268, and Xgwm456 whereas the other minor locus contributing to the quality trait was found near Xgwm106 on translocated chromosome 2B. STRs located near these genes may be used for controlling the transfer of valuable traits in new wheat cultivars.