The stem rust resistance gene Sr26 imparts resistance to all the virulent pathotypes of stem rust (Puccinia graminis f. sp. tritici) including a new race of pathogen named TTKSK (syn.Ug99). Wheat genotypes including non-carrier Kalyan Sona (-Sr26) and carrier Kite (+Sr26) of the Sr26 gene were analysed using polymerase chain reactions and a RAPD marker OPAE07620 was found to link with the desired trait. Linkage between the marker OPAE07620 and rust resistance phenotype was confirmed by analyzing F2 population obtained from a cross between a resistant and susceptible genotype. The Random Amplified Polymorphic DNA (RAPD) marker was converted into sequence characterized amplified region (SCAR) marker SCOPAE07620. The marker was validated in another segregating population and 45 wheat genotypes including carrier and non-carriers of Sr26 gene. The marker developed in this study can be used for pyramiding of the Sr26 gene with other major resistance genes that are effective against the TTKSK lineage (Ug99) which will help in attaining durable resistance against a disease that poses a serious threat to global wheat production.