The genetic diversity and molecular characterization of 10 wheatgenotypes was investigated using 27 polymorphic microsatellitescreened primers including Simple Sequence Repeats (SSR). Abouttwenty one loci were found. Bioinformatics tools were applied forconstructing dendogram. Lr-19 gene was present in all ten wheatgenotypes and Sr-15 gene is present in nine genotypes except Uqab-2000 that cause resistance against wheat rust. Highest geneticdiversity was observed between Shalimar-86 and Pak-81 genotypesand showed the similarity of about 95.34%. Distantly related Uqab-2000 showed minimum genetic diversity and 65.64% dissimilaritywith Kohistan-97. Uqab-2000 rust resistant genes may have aninsertion or deletion and examined as distantly related to rest of ninegenotypes. The current research found that SSR makers identifiedrust resistant genes in numerous wheat genotypes. Present work alsocharacterized the wheat genotypes at molecular level and foundgenetic diversity between different wheat genotypes. SSR markerscould distinguish and characterize wheat genotypes, more screenedprimers could be used for saturation of different regions in furtherresearch. Bioinformatics also play a vital role in retrieving,analyzing and interpreting the data for further studies.