The present research was carried out to investigate the genetic diversity among cowpea tolerant and susseptibe genotypes. For which the fifteen cowpea genotypes were manually infected with Cowpea yellow mosaic virus(CYMV)  inoculum and  to detect virus by a serological technique.  The five most tolerant and sensitive each genotypes had been taken for genetic diversity study in which JCPL-2 and JCPL-11 was found most susceptible and tolerant genotype, having absorbance at 405nm 2.172 and 0.167 respectively. The RAPD, ISSR and SSR marker system were applied to the ten cowpea genotypes. For the RAPD data, based on PIC value, it can be said that primer OPAI-15 was the best primer resulting good amplification with maximum PIC value (0.764).Dendrogram constructed using the RAPD data clearly distinguished all genotypes. It revealed that JCPL-44 and JCPL-45 found in one cluster and shared maximum 96.00% similarity; however, genotype JCPL-2 have out grouped from other 9 genotypes and shared minimum 41.00% similarity. In case of ISSR data, based on PIC value it can be said that the primer 835 was the best primer resulting good amplification with maximum PIC value (0.837). Jaccard’s similarity coefficient ranged from 0.625 and 0.906. The ISSR results indicated that maximum similarity 90.60% was found between JCPL-2 and JCPL-18, while minimum similarity 62.50% was obtained between JCPL-2 and JCP- 87. For the SSR data, based on PIC value it can be said that the primer VM-13 was the best primer resulting good amplification with maximum PIC value (0.668). Jaccard’s similarity coefficient ranged from 0.500to 1.000. So SSR data revealed that JCPL-2 showed maximum variability compared to other nine genotypes. The combined RAPD, ISSR and SSR analysis revealed that out of ten genotypes JCPL-44 and JCPL-45 were showed maximum (91.0%) similarity. The lowest similarity of 58.30% was found between JCPL-2 and JCP-45.