Wheat is the staple diet for the people of Pakistan and covered larger than any other cereal crop area in Pakistan. Among biotic stresses, stripe rust is the most important disease and appears every year in the country. To study the virulence spectrum of yellow rust under field conditions in Pakistan a trap nursery was planted at eight locations, which were considered the hot spots for yellow rust development in Pakistan Two years data revealed that the virulence for stripe rust resistant genes Yr1, Y2, Yr6, Yr7, Yr9, Yr17, Yr18, Yr29 and Yr32 were common alone or in combinations while the genes Yr5, Yr10, Yr15 and YrSp were found effective. Deployments of stripe rust resistant wheat varieties are considered as reliable and environmental friendly method to minimize yield losses. To identify the resistant genes by conventional way through diversified races take a considerable time and have to maintain every year which could be avoided through the use of DNA markers. One hundred and twenty five wheat varieties/lines were screened under glass house and field condition. Dominant stripe rust race 574232 was used to screen the material and there were only two lines which had high infection type. Twelve microsatellite markers associated with stripe resistance genes were used to identify the genes present but 10 markers were produced good results. Different primers revealed variable frequency of different resistance genes. Stripe rust resistant gene Yr5 was present in 36.8% of lines shown by marker S19M97 and in 62.4% shown by markers S23M41. The marker iag95 was used to identify the yellow rust resistant gene Yr9 and was amplified in 27.2% wheat lines. Yellow rust resistant gene Yr10 was present in 87.2% lines revealed by marker psp3000. Yr17 was found in 34.4% lines as revealed by marker Venturip-LN2 and Yr18 was present in 24.8% lines as shown by marker CslV34 and in 11.2% lines as shown by cssfr5. Two microsatellite markers were utilized to identify the yellow rust resistant gene Yr26 which showed its presence in 98.4% lines by wmc419 and 82.4% lines by xgwm11. Yr29 was present in 91.2% shown through the use of marker wmc367. Considering the short time period for effectiveness of major resistance genes, QTLs were attempted to be identified in the F2 population developed by crossing Seher-06 and local white and population of 210 lines were maintained and screened under field conditions. Four hundred and fifty two SSR markers were applied to screen the parents and 183 SSR polymorphic markers were genotyped in population. A linkage map was constructed by applying polymorphic markers covering all chromosomes. A LOD value of 3 was declared as threshold to identify the QTLs. Fourteen QTLs of were mapped on chromosome 1A, 1B, 2A, 2D, 3B, 3D, 4D, 6A, 6B, 7A, 7B and 7D by different linked and flanking markers. Two QTLs were mapped on chromosome 3B and 3D each. The QTL mapped on chromosome 1A, 1B, 3B and 7D were strongly reducing the disease severity (AUDPC) and have high additive effect. The QTL identified on chromosome 7D could be considered novel as previously no QTL was mapped on long arm of this chromosome. A high LOD values in the range of 5.32 to 14.56 were observed in the population analysis. A second population of 204 RILs (AC Cutler x AC Barrie) was obtained from the University of Alberta Canada to identify the QTLs. Population was screened at different locations of Pakistan under natural and inoculated conditions during four years. There was a wide range of climatic variation among the locations and years. A QTL common on chromosome 1B was found in 105-108 cM region across all the years and locations and was considered the most persistent and provided the high level of resistance across the environments. The marker linked with this QTL was DArT marker Wpt-1770 and flanking marker was Wpt667092. Two QTLs were mapped on chromosome 1D and 2D from Nowshera. Two QTLs were mapped on chromosome 4A from Sialkot and Faisalabad at 94.5 and 96.5cM positions considered as the same. Three others QTLs were mapped on chromosome 5B from Attock and Faisalabad. Four QTLs of minor effects were mapped on chromosome 6A with different intervals at both long and short arm of chromosome. Two QTLs were mapped from Islamabad experiment at 4cM and 13cM positions. A single QTL was mapped on chromosome 7A at 17cM position linked with DArT marker Wpt8473. The stripe rust resistance genes and QTLs identified in our studies will provide the information to the breeders of Pakistan and the utilization of this data enhanced the wheat production by utilizing this data of major and minor genes.