Saraca asoca, commonly known as ‘Asoka’ or 'Ashoka,' holds significant medicinal value in India. However, due to the escalating demand in the herbal market, the species has suffered a severe decline in naturally occurring populations, primarily caused by the unregulated extraction of its wood. Particularly within the Western Ghats, a global biodiversity hotspot, the species faces critically low population sizes. The study addresses a highly relevant conservation concern, focusing on an ecologically and culturally important species within a global biodiversity hotspot. Twelve populations in the Western Ghats were analyzed using five highly polymorphic and newly developed microsatellite markers. The results revealed a total of 78 alleles, with an average of 15.6 alleles per locus across the twelve populations. The AMOVA analysis indicated that the species exhibits higher diversity within populations (91.38% variation) compared to the variation observed among populations (8.62%). Further analysis employing Bayesian clustering identified six distinct genetic clusters within Saraca asoca. Based on these genetic findings, strategies for the development of an in-situ conservation plan for the species have been formulated. Overall, this study sheds light on the genetic characteristics of Saraca asoca populations in the Western Ghats and provides valuable insights for the implementation of effective conservation measures.