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Prosopis cineraria (L.) Druce, commonly called khejri, is an important multipurpose, leguminous tree of the Thar Desert. ’Thar Shoba’ is a variety of khejri without thorns which was developed as a vegetable. In order to develop markers for varietal identification, 80 RAPD primers were tested, of which nine were polymorphic between ’Thar Shoba’ and trees in a natural population of khejri. Phenetic analysis revealed that ’Thar Shoba’ formed a separate cluster from the natural population with similarity coefficients of 0.57-0.78. The 10-mer primers OPBE05, OPBA13, OPA12, and OPA14 were each found to differentiate ’Thar Shoba’ from the natural population by one amplicon. These differential amplicons were sequenced and SCAR markers were developed based on the sequences that differentiated ’Thar Shoba’ from the natural population. Natural populations of khejri from different regions of the Thar Desert, and clonally multiplied ’Thar Shoba’ plants in the ICAR-CIAH bud-wood genebank, were used to validate these primers. These markers will be useful in further developing the bud-wood genebank, and for certification, identification, and protection of the khejri variety ’Thar Shoba’.