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Bacterial canker of stone fruits caused by Pseudomonas syringae pv. syringae (Pss) and Pseudomonas syringae pv. morsprunorum (Psm race‐1/Psm race‐2) may lead to significant yield and crop losses in apricot (Prunus armeniaca L.) cultivation areas in Türkiye. Strains pathogenic to apricot were isolated from trees with symptoms (mainly necrotized buds and dieback) of bacterial canker in orchards in Aras Basin. Pathogens were characterized using pathogenicity tests, phenotypic assays, end‐point PCR and multilocus sequence analysis (MLSA). Fifteen Pseudomonas syringae strains were isolated from 205 plant samples collected from apricot orchards showing symptoms of bacterial canker. As a consequence of the diagnostic tests, all isolates were identified as P. syringae pv. syringae. In this study, Pss, Psm R1 and Psm R2 strains in stone fruits were separated into different phylogroups (Pg‐2, Pg‐3, sPg‐1b) based on MLSA. Turkish strains obtained from stone fruits, particularly apricot, showed genetic heterogeneity, and clustered in different sub‐phylogroups (sPg‐2b, sPg‐2c, sPg‐2d). All these strains except strain K258 are also clustered in the same sub‐phylogroups (sPg‐2b and sPg‐2d) with other strains from different countries especially Iran, Lebanon, etc. Strain K258 isolated from apricot was clustered in sPg‐2c with Pss strain 642 (USA). The risk of bacterial canker disease in apricot growing areas is considered using GIS in this study. It was determined that a significant part of the Iğdır Plain, the biggest agricultural area in the Aras Basin, is at very high risk. [ABSTRACT FROM AUTHOR]