In this study, Synthetic Hexaploid lines of Wheat viz., Syn 4, Syn 55 and Syn 86 were screened for resistance against virulence stem rust pathotype 40A at Division of Genetics, IARI, New Delhi. The nature of inheritance of gene governing the resistance in these synthetic lines and their allelic relationship were studied. The gene for resistance in Syn 4 and Syn 55 was found to be same, as confirmed by the test of allelism. In Syn 86. The resistance to stem rust was governed by two genes one dominant and one recessive). The F2 population developed from a cross between Syn 4 x Agra local, was used to identify molecular marker linked to stem rust resistance gene. A total of 75 RAPD’s and 35 SSR primer pair were selected covering D-Genome and B-Genome on the basis of chromosomal location of resistance gene. The SSR marker Xgwm533 was found to be linked with resistance gene at a distance of 5cM and marker Xgwm389 was co-segregating. Xgwm533 was taken from B-Genome hence, the resistance gene to be located on 3-B Genome of wheat. The use of these markers in combination with other marker could better predict the presence of gene for resistance to stem rust in breeding population.