Wheat stem rust, caused by Puccinia graminis Pers.: Pers f. sp. tritici Eriks. & E. Henn. (Pgt), is a destructive disease that can cause severe yield losses in wheat. A new Pgt race Ug99 (TTKSK), which was first identified in Uganda in 1998, has overcome many important stem rust resistance (Sr) genes. There is an ongoing world-wide need to identify new and effective resources of resistance. The objectives of this study were to transfer the Ug99-effective Sr genes from wheat-grass species Thinopyrum junceum to hexaploid wheat through chromosome engineering and to identify and map new Sr genes from tetraploid wheat Triticum turgidum ssp. carthlicum. A wheat ‘Chinese Spring’ (CS) –Th. junceum disomic addition line, HD3505, was identified to be resistant to Pgt races in the Ug99 race group. We transferred the Sr gene from HD3505 into CS through chromosome engineering. I identified three BC2F1 plants with reduced Th. junceum chromatin (BG2133, BG5136, and BG2161) carrying the stem rust resistance. This new gene is located on a wheat group-4 chromosome based on the molecular data. To identify and map the new Sr genes in tetraploid wheat, a population of 190 recombinant inbred lines was developed from a cross between T. turgidum ssp. carthlicum (PI 387696) and susceptible durum wheat line Rusty. This population was screened with TTKSK, TRTTF, and TMLKC and genotyped using the wheat 90K iSelect array. A major QTL was identified and mapped to the genomic region harboring the Sr13 locus on 6AL. Molecular markers for Sr13, including BE403950, CK207347 and KASPSr13, indicated that resistance in PI 387696 was due to the Sr13 gene. But evaluation of genetic stocks carrying Sr13 with specific races at different temperature conditions indicated that resistance in PI 387696 is due to new allelic form of Sr13 or due to other novel Sr gene close to Sr13 locus. The marker validation showed that two newly-developed STARP markers Xrwgsnp6 and Xrwgsnp7 can be used for marker-assisted selection of Sr13 in wheat breeding programs. The novel genes or alleles identified in this research provide resistance against TTKSK and other emerging Pgt races and they can be used in wheat improvement.