Abstract Eremostachys superba Royle ex Benth. (Lamiaceae) has undergone a severe decline in population size since its discovery in the North-western Himalayas in late 19th cen- tury. One hundred and seventy-two plants from six populations in the Indian states of Uttar Pradesh and Jammu & Kashmir, located be- tween 0.45 km and 455.72 km apart from each other were evaluated for RAPD polymorphism. Sixteen random primers generated 92 bands overall, 77 of which were polymorphic. Shan- non’s index of genetic diversity within popula- tions (H o ) ranged between 0.305 and 0.421; the average within-population diversity (H pop ) was 0.389; and the total species diversity (H sp ) was 0.478. The population from Mohand (represent- ing the type locality) had the fewest plants, at 18, and was genetically the most depauperate. Among the other populations, ranging in size between 52 and 1,022 individuals, no relation between population size and genetic diversity was evident. It is suggested that these six populations represent relics of a larger, extended population, in which the presence of perennating rootstocks has helped preserve historic patterns of genetic diversity. AMOVA revealed that 83.01% of the variation exists within popula- tions, which was consistent with earlier studies on the reproductive biology of E. superba, which indicated this species is predominantly alloga- mous. FST distances between all populations were significant, indicating geographic differen- tiation despite some of them being closely separated. Habitat restoration and protection from indiscriminate harvesting are proposed as primary strategies for conserving E. superba. Rejuvenation of the Mohand popu- lation through intrapopulation crossing between plants bearing diverse molecular phenotypes is also suggested. Keywords AMOVA Æ Conservation Æ Genetic distance Æ Population genetic structure Æ Shannon’s index S. Verma (&) Æ A. K. Koul Post Graduate Department of Biotechnology, University of Jammu, Dr. Baba Sahib Ambedkar Marg, Bahu Wali Rakh, Jammu, J&K 180006, India e-mail: eremurus@rediffmail.com J. L. Karihaloo Asia-Pacific Consortium on Agricultural Biotechnology, CG Centres Block, DPS Marg, New Delhi 110012, India S. K. Tiwari NRC DNA Fingerprinting, NBPGR, Pusa Campus, New Delhi 110012, India R. Magotra Post Graduate Department of Botany, University of Jammu, Dr. Baba Sahib Ambedkar Marg, Jammu, J&K 180006, India Genet Resour Crop Evol (2007) 54:221–229 DOI 10.1007/s10722-006-9118-0 123 SHORT COMMUNICATION Genetic diversity in Eremostachys superba Royle ex Benth. (Lamiaceae), an endangered Himalayan species, as assessed by RAPD Susheel Verma Æ Jawahar L. Karihaloo Æ Shailesh K. Tiwari Æ Rani Magotra Æ Awtar K. Koul Received: 25 March 2006 / Accepted: 4 September 2006 / Published online: 30 December 2006 Ó Springer Science+Business Media B.V. 2006