Stone fruits are the major source of livelihood in some areas of Khyber-Pakhtunkhwa (KPK) Province, Baluchistan Province and northern areas of Pakistan. According to the production data of Food and Agriculture Organization (FAO), 2014 Pakistan ranked 6th in apricot production all over the world, but the production of apricot and plum was decreased to thousands of tons from 2012 to 2014 (FAO, 2014). Several biotic and abiotic constrains involved in low production of peach, apricot and plum. Regarding biotic factors bacterial diseases especially bacterial canker of stone fruits have major concern, it has been reported from almost all the countries producing stone fruits. However, in Pakistan no work has been done on pathological aspects of stone fruits. Depending on that scenario this study was proposed to determine the incidence and prevalence of bacterial canker disease in KPK and Punjab provinces of Pakistan. There was 100 % prevalence found in both the provinces of Pakistan and incidence of bacterial canker varies in different districts of KPK and Punjab but found that incidence was increased in every orchard in every location of Punjab and KPK in 2nd year (2016). Highest disease incidence was in peach and apricot orchards of Murree area (Province Punjab) that was 66 and 54 % respectively in 2015. However, the disease incidence increased to 71 and 56 % respectively in 2016. In plum orchards highest disease incidence was in Soan valley (54 %), it also increased (57 %) in 2016. Similarly, in KPK province highest disease incidence in peach and apricot was in Swat i.e., 69% and 72% in 2015, next year it also increased to 75 and 67% respectively. In plum orchards highest disease incidence was in Nowshera that was 67% in 2015 and 71% in 2016. Pathogen was isolated from the infected samples (leaf, fruit and gum) and 64 isolates with gram negative having positive loop test results and also showed fluorescence under UV light were screened out as Pseudomonas spp. Pathogenicity was done to check the pathogenic behavior of isolates and 43 isolates found pathogenic that develop sunken canker symptoms on fresh peach fruit and remaining isolates were discarded. During syringomycin bioassay isolates 32 isolates were found to be pathovar syringae that develop clear zone of inhibition from 1mm to 15mm. All pathogenic isolates were subject to biochemical characterization using LOPAT and GATTa scheme and L-lactate utilization test. Again results were similar 11 isolates showed confusing results. Further molecular characterization was done to identify pathovars and races using universal (16S rRNA) primer and one house keeping gene (gyrB gene) primer. Phylogenetic analysis was done using Molecular Evolutionary Genetics Analysis (MEGA) version 7 and it was found that 32 isolates were P. syringae pv syringae and the remaining isolates were P. syringae pv. morsprunorum race 1. There was no pathovar morsprunorum race 2 isolate found from all the visited districts of KPK and Punjab provinces of Pakistan.