Cluster bean, one of the most important cash legume crop has played an increasingly important role in wide range of industries. Owing to the significance of molecular marker studies in numerous applications including in genetic improvement of crops, there is an obvious need to undertake such studies in cluster bean. In the present work, 35 genotypes of cluster bean were collected from different states of India and analyzed using RAPD and ISSR markers. Further SCAR marker system was introduced in order to increase the reproducibility of the polymorphism and specificity. For this polymorphic (RP-3, 1000 bp; RP-19, 1250 bp and 1100 bp) and geographical specific bands (RP-9, 650 bp) from RAPD as well as genotype specific band (IS-8, 550 bp) from genotype RGC-1031 (Rajasthan) from ISSR were selected and converted into SCAR markers. The study revealed first set of sequence-based SCAR markers in cluster bean which found more specific information using RAPD and ISSR profiles. One genotype specific SCAR-20 for RGC-1031 (tolerant genotype against Macrophomina phaseolina), could be used to prove identity of the genotype for improvement as well for its genetic purity assessment. Another SCAR-8 was selected due to its specificity for cluster bean genotypes from Rajasthan which might be important for population admixture studies.