Abstract: The strength of any ongoing breeding programme thoroughly depends on the presence of genetic variation at both morphological and molecular level. In present study, total 36 pearl millet genotypes were evaluated for different morphological characters along with grain Fe and Zn contents. High estimates of coefficient of variation inclusive of high heritability and genetic advance as per cent of mean was marked for dry fodder yield per plant, grain yield per plant, Fe and Zn contents. This suggested that the selection based on these traits will be effective in improving breeding material. Further correlation analysis showed a highly significant correlation between grain Fe and Zn content which signifies simultaneous improvement in the two traits. Grain yield per plant showed nonsignificant negative correlation with Fe and Zn thus suggesting improvement in nutrient value without sacrificing yield. A set of 64 SSRs was also used for molecular diversity assessment. A significant positive correlation was observed among number of alleles, Polymorphic Information Content (PIC) and number of repeats in the SSR motifs. Across the linkage groups, the mean PIC varied from 0.48 (LG 3) to 0.76 (LG 2). Mean alleles per locus and overall PIC obtained was 7.20 and 0.68 respectively. Presence of ample variation at morpho-genetic level signifies their use as parents in the out crossing programmes to obtain new improved hybrids with desired traits.