Xanthomonas axonopodis pv. cyamopsidis causes bacterial blight of cluster bean, an industrially important legume. A total of 76 isolates of X. axonopodis pv. cyamopsidis obtained from cluster bean fields of north and north-west India were identified at the pathovar level using virulence trials on the susceptible cluster bean genotype, PNB which confirmed their phytopathogenic specialization on cluster bean. Different polymerase chain reaction (PCR)-based techniques, such as, random amplified polymorphic DNA (RAPD)–PCR, repetitive (rep)-PCR and IS1112-PCR were successfully employed to elucidate the pathogen population structure and intrapathovar relationship among a set of 25 X. axonopodis pv. cyamopsidis isolates. There was a significant variation in their pathogenicity and genetic structure. The pathogenicity data were found to be in line with the molecular data to some extent. RAPD markers revealed a high level of genetic diversity across the isolates employed in comparison with the other molecular markers employed. A weak correlation was observed among the various molecular markers employed as each technique explores genetic variation differently. There was no correlation between DNA amplification product patterns and geographic sites of isolation, suggesting that this bacterium has spread largely through exchange of infected plant germplasm. This is the first report on the molecular characterization of X. axonopodis pv. cyamopsidis isolates from India.