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To ascertain the conservation priorities and strategies for Commiphora wightii, an endangered medicinal plant of Indian Thar Desert, genetic diversity was estimated within and among different populations. The total of 155 amplification products were scored using ten each of RAPD and ISSR primers, exhibiting an overall 86.72% polymorphism across 45 individuals representing eight populations. The cumulative data of two markers were used to compute pair-wise distances. The Neighbor-Joining tree revealed high genetic differentiation among populations except Kiradu population. Nei’s gene diversity (h) ranged between 0.082 and 0.193 with total diversity at species level is 0.294. Shannon’s information index (I) ranged between 0.118 and 0.275 with an overall diversity of 0.439. Analysis of molecular variance showed more diversity among population level (56.65%) than at within population level (43.35%). The low gene flow value (Nm = 0.349) and high coefficient of genetic differentiation (G(ST) = 0.589) and high fixation index (F-ST = 0566) demonstrated elevated genetic differentiation among the population and can be predicted that these populations are not in Hardy-Weinberg proportions. Principal Coordinate Analysis confirms that Akal population has become phylogenetically more distinct and less diverse than the rest of the samples. Mantel’s test revealed no correlation between genetic and geographical distances of populations (R-2 = 0.122). Overall highest diversity was observed in the population of Machiya Safari Park and Kiradu, while lowest in Akal population, later may constitute an evolutionary significant unit, having merit for special management. (C) 2013 Elsevier B.V. All rights reserved.