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Prosopis cineraria, an important multipurpose tree and vital component of the otherwise fragile ecosystem of arid and semiarid regions of India. It is highly drought tolerant and sprouts profusely during the extreme dry summer months when most other trees are leafless. P. cineraria is known to exhibit comparable genetic variations at intra-specific and inter-population levels reflected through morphological and cytogenetical diversity in regions, where this plant grows naturally. In the present study, single primer amplification reaction (SPAR) methods have been used for determination of diversity at DNA level in 30 accessions of P. cineraria collected from different districts of Rajasthan. The analyses include the use of six minisatellite core sequence primers for direct amplification of minisatellite DNA (DAMD), eight inter simple sequence repeats (ISSR) and 20 arbitrary primed decamer sequences for random amplification (RAPD) reactions. Upon analysis of the data generated, all the three SPAR methods, either independently and/or in combination, revealed wide range of genetic variation among accessions. Comparison of matrix of individual SPAR method using MxComp component of NTSYS-pc 2.02 K software proving that analysis of natural genetic variation using combination of SPAR methods particularly ISSR and DAMD, rather than an isolated approach, is very effective. Such an approach also yields better information and reflection of the relatedness and affinities at intra-species and inter-population levels. Therefore, it is opined that in order to reveal the intrinsic intra-specific variation, SPAR approaches involving more than one DNA marker may reveal more authentic genetic variation in tropical tree species like P. cineraria.