Stripe rust, caused by Puccinia striiformis Westend f. sp. tritici, is a devastating disease of wheat affecting its production and livelihood of millions of farmers worldwide. Diversity is an important component of sustainable crop improvement program. Diverse panel of genotypes provides the breeder best options for selecting superior parents to utilize them directly in resistance breeding. Keeping this in mind, a diverse panel of yellow rust resistant and susceptible genotypes consisting of 6 durum, 2 diccocoids, 4 triticale and 56 bread wheat elite lines ware screened with yellow rust linked SSR markers to assess the allelic variation among them. For this, a total of 72 molecular markers were screened, out of which 51 amplified whereas 38 were highly polymorphic and 6 were monomorphic. Furthermore, considerable genetic variability was observed among wheat genotypes on screening with 38 highly polymorphic SSR loci. A Total of 115 alleles were scored and the number of alleles per locus varied from 2 to 8 with an average of 3.02 alleles per locus. Maximum 8 alleles were identified in marker Xgwm273 and Wmc44. The PIC values ranged from 0.0 to 0.872 with an average value of 0.534 among SSR loci. Maximum PIC (0.872) was identified in Xgwm582 followed by (0.789) in Xgwm526. Least PIC (0.0) was found in S26M49 and Owm45F3R3 followed by (0.1) in Xgwm533. Estimates of genetic distance based on Jaccard’s similarity coefficients ranged from 0.58 to 0.95 indicating the wide range of genetic diversity at genotypic level. Two-dimensional PCA and Three-dimensional PCA analysis also showed the clustering of yellow rust susceptible and resistant genotypes into separate groups suggesting the wide diversity among wheat lines. In addition to that, molecular marker-based gene identification showed the presence of Yr genes in various frequencies. Genes Yr26 (69.2 %), Yr2 (69.1 %), Yr64 (61.7 %), Yr24 (58.9 %), Yr7 (52.9 %), Yr10 (50 %) and Yr 48 (48.5 %) showed high frequency among selected wheat genotypes, while Yr9 (2.94 %), Yr36 (2.94 %), Yr60 (1.47 %) and Yr32 (8.8 %) were least frequent in wheat genotypes. Under epiphytotic conditions, coefficient of infection ranged from 0-60 among all wheat genotypes. Fifty three genotypes were found resistant (ITs 0), accounting for 77.94% of total genotypes, 3 genotypes (4.4%) showed trace resistance (ITs 1), 7 genotypes (10.3) were moderately susceptible (ITs 3) and 5 genotypes (7.35 %) were susceptible (ITs 4). Differential lines carrying avirulent Yr5, Yr10, Yr15, Yr24, Yr26 showed good immune response at field testing. These lines can be further directly utilized in the molecular breeding programme for yellow rust resistance.