Rice is important for sustainable food and nutritional security; however, nominal micronutrient quantities in grains aggravate malnutrition in rice-eating poor populations. In this study, we evaluated genetic diversity in grain iron (Fe) and zinc (Zn) contents using trait-linked simple sequence repeat (SSR) markers in the representative subset of a large collection of local and exotic rice germplasm. The objective of the study was to evaluate genetic variability parameter and discern correlation for Iron (Fe) and Zinc (Zn) content in grains of different RPHP rice accessions grown in Kharif-2012 under aerobic condition. Single molecular marker analysis using 19 SSR markers showed that RM1089 and RM144 were associated with grain Fe and Zn content respectively. The genetic information generated and molecular markers identified from this study may be used for future biofortification programme of rice.