Dysoxylum binectariferumHook.f (Meliaceae) is a medicinally important medium to large-sized tree species found intropical and subtropical regions. This species is distributedin the Western Ghats of southern India and is well knownfor its wood (Rao et al.1961). It has gained considerableinterest in recent years because of the pharmacologically important compound rohitukine and its derivativeflavopiridol. Rohitukine, a chromane alkaloid, is reported topossess anti-inflammatory, anti-fertility, anti-implantation,anti-cancer and immuno-modulatory properties (Naiket al. 1988;Carlsonet al. 1996; Sedlacek et al. 1996;Mohanakumaraet al.2010). Dysobinin, the other chemicalcompound isolated from fruits of this tree is also reported toexhibit significant central nervous system depressant actionand mild anti-inflammatory activity (Singhet al.1976). Thebark is also reported to be used for the treatment of leprosyand foul ulcers (Jain and DeFilipps1991).This species is threatened throughout its range in Western Ghats as a result of overexploitation and habitat destruction, which have reduced local population sizes and has ledmany populations to local extinction. In this study, we reportthe development of microsatellite markers and discuss theutility of these markers in addressing questions related to thepopulation and conservation genetics of this species.