The present study was carried out for the comparison of ISSR and RAPD markers for polymorphism pattern andmolecular diversity analysis among ten cowpea (Vigna unguiculata L.) genotypes. Out of 50 ISSR primers, 18 primers produced total 103 bands across ten cowpea genotypes, of which 49 bands were polymorphic. A maximum polymorphism (85.70%) was obtained by UBC 815. Average numbers of polymorphic bands per UBC primer was 2.72. The UBC 834 was the best primer resulting good amplification with maximum PIC value (0.890). However, out of 50 RAPD primers,

14 RAPD primers produced 120 bands across ten genotypes, of which 81 bands were polymorphic. A maximum polymorphism (90.0%) was obtained with OPV-16 primer. Average number of polymorphic bands per RAPD primer was 5.78. The primer OPD-08 was the best primer resulting good amplification with maximum PIC value (0.923). Jaccard’s similarity coefficient ranged from 68.40% to 92.90% for ISSR, for RAPD are 57.10% to 81.00% and for ISSR-RAPD coefficient data ranged from 85.70% to 63.50%.