Wheat is the major cereal crop in India on which the food security rests. Determination of the best selection criteria is the most important aim in wheat breeding programs. To achieve high yield potential in wheat, hybrid breeding is a major innovative technique. A total of 16 newly developed CMS lines and a restorer lines, were used as the experimental material. Out of 82 pairs of SSR marker, Six SSR markers viz. Xcdf23, Xgmw374, Xgwm371, Xgwm335, Xwmc285 and Xwmc617, were analyzed for confirming that, the male sterility is controlled by a single dominant Ms2 gene in sixteen male sterile parental lines. Sixteen maintainer parental line were amplified with four SSR markers Xwmc131, Xwmc503, Xwmc44 and Xcdf63 to exhibit the Rf3 fertility restoration gene. Rf3 gene controls fertility in maintainer and hybrid lines and was found to be linked with the four SSR markers. The parental polymorphism survey indicated that four SSR markers viz., Xwmc346, Xbarc61, Xgwm294-2A, and Xgwm46-7B gave clear cut differentiation in both the (male and female) parents and indicated polymorphism among them, which confirm the authentication of hybrids.