Genetic diversity among 48 ber genotypes from different eco-geographical regions of India was investigated using random amplified polymorphic DNA (RAPD) and intersimple sequence repeat (ISSR) markers. Forty-six RAPD and 18 ISSR primers generated a total of 368 and 167 amplification products of which 271 (74.15%) and 152 (89.94%) were polymorphic, respectively. The average numbers of polymorphic fragments were 5.89 (RAPD) and 8.44 (ISSR) per primer with number of amplified bands ranging between 2 to 17 and 4 to 12 for RAPD and ISSR respectively. RAPD primer OPD-3 (9.00 Rp and 0.29 PIC) and ISSR primer UBC-880 (5.63 Rp and 0.29 PIC) were the most informative primers. Out of the 18 ISSR primers 14 were anchored, of which 12 were 3'-anchored and 2 were 5'-anchored. Fourteen ISSR primers produced distinct bands contained dinucleotide repeats. Primers based on (AC)n and (AG)n repeats produced the most polymorphic bands. Based on mantel matrix correlation between two marker systems it is suggested that the two markers amplify different genomic regions. The genetic similarity among 48 ber genotypes ranged from 47.62% (Thornless and Seov) to 88.97% (Narma and Banarsi Karaka) that suggested a wide genetic base for the ber germplasm collection. The study suggests superiority of ISSR marker system over RAPD for studying genetic diversity in ber.