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Prosopis cineraria (L.) Druce, family Fabaceae, is an important multipurpose tree species of the Indian Thar Desert. It is an extremely drought and heat tolerant plant and has ability to survive in highly alkaline and saline environments. Considering the commercial, horticultural and ecological importance of P. cineraria, there is a great need to develop genomic resources in the form of microsatellite markers for the genetic enhancement of this crop. We identified and characterized 10 microsatellite markers in P. cineraria by cross species amplification. Total 18 Simple Sequence Repeat (SSR) primer pairs developed in P. chilensis, P. alba, and P. flexuosa were used to amplify SSR loci in P. cineraria. Out of eighteen SSR markers tested, ten (55.5%) amplified recognizable amplicons. The number of alleles detected at each locus ranged from one to four, a total of 24 with an average of 2.4 alleles. Observed heterozygosity (Ho) and expected heterozygosity (He) values varied from 0.14 to 0.85 and 0.21 to 0.56 with an average of 0.47 and 0.37, respectively. The polymorphic information content (PIC) values ranged from 0.49 to 0.78 with an average of 0.66. Of the nine polymorphic markers, seven were highly informative and polymorphic (PIC > 0.5). These microsatellite markers are characterized for the first time in P. cineraria. All microsatellite markers identified in this study may be useful in comparative genomics and population genetics studies of P. cineraria.