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Commiphora wightii is an endangered, endemic species found in the Thar Desert of Rajasthan, India and adjoining areas of Pakistan. The populations of this plant are rapidly dwindling due to overexploitation for their medicinally important resin. Analysis of nucleotide sequences of the internal transcribed spacer of rDNAs revealed low genetic diversity (π = 0.03905; θw = 0.05418) and high population structure (ϕST = 0.206). Parsimony based assessment and Bayesian analyses were conducted on the dataset. Mantel’s test showed a statistically significant positive correlation between genetic and geographic distance (r2 = 0.3647; p = 0.023). Anthropogenic overexploitation of C. wightii for its natural resources has resulted in population fragmentation. Initiatives should be taken immediately to preserve the diversity of this important plant species.