Strains of Pseudomonas syringae pv. syringae (Pss), Pseudomonas syringae pv. lachrymans (Psl) and Pseudomonas tolaasii (P. tolaasii) were analyzed for genetic diversity. For molecular identification of the strains, three primer pairs were used. Molecular analysis was done with random amplified polymorphic DNA (RAPD) and Insertion Sequence (IS50) primers. IS50-PCR and RAPD-PCR analysis divided 51 strains into eight sub clusters that were grouped in three clusters. Cluster I comprised all Pss with four sub clusters from stone fruits, pome fruit and cereal hosts, cluster II contained Psl strains from cucumber with two sub clusters and cluster III contained three strains of P. tolaasii with two sub clusters from mushroom. These results indicated that a combination of IS50-PCR and RAPD-PCR fingerprinting can be used as a high resolution genomic fingerprinting methods for differentiates species of Pseudomonas and pathovars of P. syringae strains.