Ber, being a hardy and drought tolerant fruit crop, fits well into the marginal ecosystem of semi-arid and arid zones. Twelve ber hybrids and their parents were molecularly characterized using RAPD markers. Of the 35 random primers tested, 26 primers showed amplification of which 24 generated polymorphic bands, while 2 of the primers showed monomorphic bands. Fifteen primers amplified all the ber hybrids and their parents. Five primers (OPE-1, OPE-2 OPE-11, OPE-13 and OPA-18) amplified specific band in ber hybrid or their parent. In total, 165 bands were produced, of which 144 bands were polymorphic, while 21 bands were monomorphic. For the genotypes tested, between 2-24 bands were obtained for each primer with an average of 6.34 bands per primer. The highest number of bands that is 24 were generated by OPE-1. The amplified DNA fragments ranged from 100-800 base pair. With un-weighted group method using arithmetic mean (UPGMA) cluster analysis, twelve ber hybrids and their parents fell into two major clusters.