This study aimed to analyze phylogenetic groups, the presence of class I, II, III integrons and resistance phenotype in a collection of fifty E. coli strains isolated from urine specimens obtained from suspected cases with urinary tract infections at Thabet Hospital, During May-December 2012. The antibiotic susceptibility testing for these isolates was done by disk diffusion method. The phylogenetic groups and class I, II and III integrons were determined by multiplex PCR. Statistical analysis was done by using Mann-Whitney U-Test (Two-tailed), Chi-square (χ2) test or Fisher exact test. The results showed that 36 (72%) of the studied strains, belonged to group D, 13 (26%) strains to group A, and 1 (2%) strain belonged to group B1. Twenty one (42%) of E. coli strains carried class I integrons. Prevalence of class I integrons in group D and group A was 44.4% and 30.8%, respectively. There was no significant difference in the mean of antibiotic resistance score for strains belonged to group D and carried class I integrons and those belonged to group A and harbored the same integron class. Antibiotic resistance has ranged from 24% for gentamicin to 100% for cefazolin and erythromycin. There is a significant difference in the mean of antibiotic resistance scores for strains belonged to group D (8.4) and group A (6.5) (P = 6.2 x 10-4). Results showed that 2 large clusters depend on resistance/sensitive of strains to fluoroquinolones. Association of trimethoprim/sulphamethoxazole resistance with the D group showed statistically significant difference (P < 0.05) compared to group A. In conclusion, molecular analysis of 50 E. coli urine isolates exhibited a greater prevalence of class I integrons, a greater prevalence of phylogenetic group D, which possessed a higher resistance scores than group A. Urinary tract infections caused by such strains represent a clinical problem because of limited therapeutic options.