Eighteen isolates of Xanthomonas axonopodis pv. punicae causing bacterial blight of pomegranate collected from different agro-climatic zones of Karnataka and other parts of India were analyzed using RAPD markers. Eight RAPD primers viz., P27, P54, P81, P59, OPG10, OPG11, OPK 07 and OPK 12 were screened in the present study. Total of 90 marker levels were obtained from all eight primers. A highest number of 15 marker levels were produced by the primer OPG-10 while 14 marker levels were produced with P-54, and a lowest of 7 marker levels were observed in OPK-12 primer. On an average 11 levels per primer was generated. Based on the result of cluster analysis, 18 isolates were grouped into two major clusters. The first major cluster included all isolates except GbF, BgL and TNL, which were grouped as a second major cluster. However, at 80% distance linkage four sub clusters were formed with in the first major cluster. Thus the isolates under study were grouped into two lineages and four races/ strains.