After decades of effective wheat stem rust control, due mainly to use of the Sr31 resistance gene in wheat, as of the early 2000s new virulent strains of the stem rust fungus, especially the Ug99 or the TTKSK races, are spreading and overcoming the resistance of commercial varieties worldwide, including the Sr24 and Sr36 resistance genes in Kenya. To address this, researchers are working to identify new resistance sources and to develop and release new high-yielding, resistant and adapted varieties. In this study we evaluated 707 advanced spring wheat lines and varieties for adult plant resistance (APR) to stem rust at the Njoro research station of the Kenya Agricultural & Livestock Research Organization, using a modified Cobb’s scale, and for seedling resistance at the Cereal Disease Laboratory (CDL), University of Minnesota, using the 0-4 Stakman et al. (1962) scale. We found 101 lines that showed APR and, through molecular marker analysis, identified 18 lines carrying the stem rust resistance marker allele for the Sr25/Lr19 gene. Of these 18 lines, 11 were resistant to Ug99 at both the seedling and adult stages and 7 were susceptible at the seedling stage, showing infection type (IT) 3 to 4, and moderately susceptible at the adult plant stage. Another 20 lines were resistant at all stages of development, without Sr25/Lr19 marker allele indicated the possibility of carrying other genes for stem rust resistance. We shared the results with national program breeders and scientists in Pakistan to facilitate the use of resistant lines in crossing programs and enhance stem rust resistance in candidate wheat varieties. As a result number of lines resistant to Ug99/ and its variants (TTKSK, TTKST) have been identified and released as commercial varieties, including NR-397 (Pakistan-2013) and NR-356 (NARC-2011).