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Genetic linkage maps facilitate the genetic dissection of complex traits and comparative analyses of genome structure, as well as molecular breeding in species of economic importance. Isabgol [Plantago ovata (Forsk.)], a medicinal plant with potent laxative properties is used in several traditional systems of Medicines and cultivated in India. We explored the DNA sequences of Isabgol in the Genbank (NCBI) and developed over 1500 simple sequence repeats (SSR) markers. Some of them were validated through DNA amplification. Transferability of SSRs from wild Plantago species viz., P. major, P. coronopus, P. lancelolata, P. maritina and P. intermida into Plantago ovata was studied. We developed a genetic linkage map using recombinant inbred lines (RILs) population which comprises of 30 random amplified polymorphic DNA (RAPD) markers spreading across 11 linkage groups (PO-1 to PO-11) with a total map distance of 75.6 cM. The SSR markers developed will have applications in assessing the functional diversity, comparative mapping and other applications in isabgol.