Stripe rust, caused by Puccinia striiformis West-end. f. sp. tritici Eriks., is an important foliar disease of wheat (Triticum aestivum L.) worldwide. The use of genetic diversity, particularly from wild relatives, has made a significant contribution to improving wheat productivity. To identify new sources of seedling and adult plant resistance, we evaluated 263 wheat–alien introgression derivatives from Secale cereale L., Leymus mollis (Trin.) Plig., Leymus racemosus (Lam.) Tzevlev, and Thinopyrum junceiforme (Á.Löve & D.Löve) Á. Löve. Three resistance genes, Yr1+, Yr2+, and Yr9+ were postulated to be present in 7, 19, and 12% of wheat–alien introgression lines, respectively. In addition, the results suggested the gene combinations of Yr1–Yr2 (1%), Yr1–Yr32 (2%), Yr2–Yr9 (5.4%), Yr1–Yr2–Yr32 (11%), and the additional unknown resistance gene(s) being present in these materials in the respective percentages. The molecular markers Xwmc364 for Yr2 (36%), Xscm9 and Xiag95 for Yr9 (17%), and Xwmc198 for Yr32 (13%) were used to validate the presence of these Yr genes. Ninety-eight (37%) of the lines possess unknown resistance genes that could not be determined with the isolates used in this study and six (2.3%) of the lines showed seedling resistance to all isolates. The lines with the putative new resistance gene(s) will be crossed to the adapted genotypes to develop a mapping population for determining the underlying genetic basis of resistance. If these resistance genes are validated as being new, they will enhance the genetic diversity for stripe rust resistance in wheat.