Abstract: Success of semi-dwarf varieties in late 1960’s lead breeders to depend heavily on these leading to narrow genetic base in today’s rice varieties. Analysis of cultivated varieties in tropical Asia revealed sd1 gene from Dee-geo-woo-gen to be the major dwarfing source. High genetic similarity renders crop genetically vulnerable to potential epidemics. Efforts are underway to broaden the genetic base using alternate sources of dwarfing. Mutation breeding has been used to increase allelic diversity. In this study, twenty radiation induced mutants of rice (Oryza sativa L.) and parent variety WL112, showing morphological differences, were screened for variation in Simple Sequence Repeats (SSR). Thirty five polymorphic SSR primers, selected from all chromosomes of rice generated 115 polymorphic bands. Jaccard’s similarity coefficient revealed considerable genetic diversity among the mutants. The dissimilarity between the mutants was as high as 65%. The UPGMA based dendrogram showed five major clusters with sub-clusters. Mutant-specific polymorphic SSR markers either alone or in combination, were detected. Twelve mutants could be identified by using specific markers, while combination of two could identify six mutants and parent. The radiation induced mutants revealed diversity and short stature in elite background which could be used in breeding programme.