Stripe rust is one of the major limiting factors in wheat production. An objective-based breeding program was initiated at Barani Agricultural Research Station (BARS), Kohat Pakistan in 2013/14 to transfer APR genes from CIMMYT and ICARDA spring wheat lines into wheat germplasm well adapted in the conditions of Khyber Pakhtunkhwa of Pakistan. Nine high yielding but stripe rust susceptible wheat varieties were crossed in various combination with 17 CIMMYT and ICARDA wheat lines carrying stripe rust (YR) resistance genes. The resultant 79 F1 combinations were backcrossed with respective susceptible parents followed by single plant selection in F2 generation. During 2015/16, 367 segregating populations/lines were screened in multi-environment stripe rust tests sites (hotspot) within Khyber Pakhtunkhwa. Sixty-nine out of 367 lines showing adequate resistance were again screened for strip rust resistance at hot spot and in yield trial at BARS, Kohat during 2016/17. Seventy lines showed considerable resistance and were found higher yielding than check cultivars. To identify genes (Yr5, Yr9 and Yr29) responsible for stripe rust resistence using SSR/STS markers, genomic DNA was extracted from selected genotypes. PCR was performed using YrSTS7/8, Xpsp3000 and Xwmc44 markers for Yr5, Yr10 and Yr29, respectively. The results indicated the presence of Yr5 in only 6 genotypes, Yr10 in 12 while Yr29 in 13 genotypes. As all these three genes are effective against stripe rust pathogen in Pakistan, it will be an advantage to transfer them to promising lines and develop durable resistance.