Background and Aims: Uropathogenic Escherichia coli (UPEC) are a causative agent in most of the urinary tract infections (UTIs) contain pathogenic island (PAI) which expresses a multitude of virulence factors. There is not much information about the type and distribution of these islands in the phylogenic groups of E. coli causing UTIs in different regions of Iran. In this study, the distribution of the Pathogenicity island (PAI) markers infections was investigated among phylogenic groups of E. coli isolates collected from patients with UTIs using Multiplex-PCR method. Materials and Methods: In this descriptive study, 100 isolates of E. coli collected from previous studies were conducted to determine the frequency of pathogenic islands and their distribution among phylogenic groups. In this method, genomic DNA of isolates was extracted by boiling method. Determination of the frequency of pathogenic islands was performed using Multiplex-PCR method. The results were analyzed using Fisher’ s exact test. Results: The prevalence of PAI IV536, PAI ICFT073, PAI IICFT073, PAI II536 and PAI IIJ96 was 84%, 44%, 30%, 16% and 9%, respectively. The PAI I536 and PAI IJ96 pathogens were not observed in any of the isolates. The highest distribution of PAI IV536 island between phylogenetic groups B2 and D was 88% (46 out of 52) and 100% (19 out of 19), respectively. Conclusions: In this study, isolates belonging to groups B2 and D were found to be the most pathogenic islands; therefore, they could play a more effective role in urinary tract infection than other phylogenic groups.