The emergence of a new highly virulent race of stem rust (Puccinia graminis tritici), Ug99, rapid evolution of new Ug99 derivative races overcoming resistance of widely deployed genes, and spread towards important wheat growing areas now potentially threaten world food security. Exploiting novel genes effective against Ug99 from wild relatives of wheat is one of the most promising strategies for the protection of the wheat crop. A new source of resistance to Ug99 was identified in the short arm of the Aegilopssearsii chromosome 3Ss by screening wheat- Ae. searsii introgression libraries available as individual chromosome and chromosome arm additions to the wheat genome. For transferring this resistance gene into common wheat, we produced three double-monosomic chromosome populations (3A/3Ss, 3B/3Ss and 3D/3Ss) and then applied integrated stem rust screening, molecular maker analysis, and cytogenetic analysis to identify resistant wheat-Ae. searsii Robertsonian translocation. Three Robertsonian translocations (T3AL·3SsS, T3BL·3SsS and T3DL·3SsS) and one recombinant (T3DS-3SsS·3SsL) with stem rust resistance were identified and confirmed to be genetically compensating on the basis of genomic in situ hybridization, analysis of 3A, 3B, 3D and 3SsS-specific SSR/STS-PCR markers, and C-banding. In addition, nine SSR/STS-PCR markers of 3SsS-specific were developed for marker-assisted selection of the resistant gene. Efforts to reduce potential linkage drag associated with 3SsS of Ae. searsii are currently under way.