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The present investigation targeted the foxtail millet Var. Srilakshmi for a high yielding attributes. The Variety Srilakshmi was irradiated with lethal dose of 400 Gy and post treated with 0.1% EMS at different time intervals of 6,12,18,24 hrs. The mutagenic concentration, (400 Gy + 18 hrs 0.1% EMS) found to be the best which leads significant increase in tiller and panicle number. The molecular profiling of selected promising mutants for tillering architect were then characterized using 27 SSR primers with 17.33% polymorphism, PIC (Polymorphic Information Content) value ranged from 0.37 to 0.69 with an average value of 0.31 and marker named SiGMS 12845 showed 100% polymorphism. The dendrogram was constructed based on SSR’s profiling and mutants were grouped into three cluster. The SSR’s markers were found to be helpful to determining the genetic diversity among mutants.