<p>Little millet is a promising cereal which can be helpful in mitigation of micronutrient malnutrition. But it is one of the least focused crops and lacks genomic resources, which hinders its adequate utilization. Since, cross genome transferability is the most cost-effective method of SSR marker development, the present study was carried out to develop genic SSR markers for little millet using iron and zinc transporter genes of foxtail millet. A total of 36 genic SSR markers were successfully designed using 4 iron and 17 zinc transporter genes of foxtail millet. Most of the markers had trinucleotide repeat motif. 20 of these markers were found to be transferable to little millet. The markers were found to be polymorphic having average PIC value of 0.58. The markers produced distinct banding pattern and had average polymorphism percent of 28. The Dice similarity coefficient value ranged from 0 to 0.72. The SSR marker-based clustering of the 26 little millet genotypes using SHAN and Principal Coordinate Analysis, were able to differentiate high and low iron and zinc containing genotypes into separate groups. The study thus reports a panel of 36 novel genic SSR markers for foxtail millet which can be used for characterization of foxtail millet genotypes based on their iron and zinc content. It also reports a panel of 20 novel genic SSR markers for little millet genotypes which can be utilized for molecular profiling of the genotypes especially with respect to their iron and zinc content.</p>