World wheat production is currently threated by stem rust (caused by Puccinia graminis f. sp. tritici) Ug99 race (TTKSK). The ongoing global effort to combat Ug99 is focusing on the identification and deployment of Ug99-resistant genes (Sr) into commercial cultivars. The objectives of this study were to identify TTKSK-effective Sr genes in untapped durum and common wheat germplasm and introgression of TTKSK-effective Sr genes from tetraploid wheat (Triticum turgidium) and Aegilops tauschii into hexaploids through production of synthetic hexaploid wheat (SHW). For identification of TTKSK-effective Sr genes, 177 durum and common wheat cultivars and lines were first evaluated using three highly virulent races TTKSK, TRTTF, and TTTTF and 71 cultivars and lines with TTKSK resistance were identified. The TTKSK-resistant cultivars and lines were then evaluated using six local races and the molecular markers that are diagnostic or tightly linked to the known TTKSK-effective Sr genes. The race specification and marker analysis showed that several previously deployed TTKSK-effective Sr genes such as Sr2, Sr24 and Sr42 were present in some of the cultivars and lines. A number of resistant cultivars and lines derived from wheat relatives such as Thinopyrum ponticum, Th. elongatum, Th. intermedium, and Ae. speltoides may carry novel Sr genes. For SHW development, 200 new SHW lines were developed by crossing 181 tetraploid wheat accessions to 14 Ae. tauschii accessions. Sixty-six of the new SHW lines, 14 previously-developed SHW lines, and their parents were evaluated for resistance to TTKSK, TRTTF, TTTTF and six other races and genotyped using molecular markers linked to the known genes in T. dicoccum and Ae. tauschii. The evaluation data showed that 44 SHW lines were resistant to TTKSK. The race specification and marker analysis showed that Sr2 from T. dicoccum and Sr33 from Ae. tauschii were present in some of the SHW lines and a number of SHW lines have novel genes conferring TTKSK resistance. The durum and wheat cultivars and lines and SHW lines with known and novel Sr genes conferring resistance to TTKSK will be useful resources for improving wheat resistance to TTKSK and other emerging races of stem rust.