Abstract The most destructive pathogen of pomegranate, Xanthomonas citri pv. punicae (Xcp), causes bacterial blight or oily spots affecting quality and quantity of pomegranate production worldwide. Different Xcp isolates obtained from geographically distant regions exhibit remarkable similarities based on multi-locus sequence analysis (MLSA) and SSR marker-based analysis. These isolates can be grouped into just four sequence types (ST1-4) highlighting the clonal nature of the pathogen.