Background: This study was set to detect extended-spectrum beta-lactamases (ESBLs) producing E. coli isolates and the genes underlying their resistance in relation to phylogenetic background from fecal samples of healthy owned cats. Methods: A total of 50 E. coli isolates were confirmed by standard bacteriological tests. The phylogenetic analyses of the isolates were carried out by combinations of three genetic markers chuA, yjaA and DNA fragment TspE4.C2 by a triplex PCR method. The ESBL (blaCTXM, blaTEM, blaSHV, blaOXA) encoding genes were detected. To identify ESBL producing phenotypes, all selected isolates were screened with a double disk synergy test including cefotaxime, cefotaxime with clavulanic acid, ceftazidime and ceftazidime with clavulanic acid. Results: Results showed that E. coli isolates fell into four phylogenetic groups (A, D, B1 and B2) with prevalence of 78%, 4%, 8%, 10% and five phylogenetic subgroups including A0 (74 %), A1 (4 %), B1 (8 %), B2–2 (6 %), B2–3 (4 %) and D1 (4 %), respectively. Among all E. coli isolates, 4% were positive for blaSHV, blaCTX-M-15 and blaOXA-1 genes which distributed in B2-2, B2-3, A0 subgroups, respectively. According to antibiotic susceptibility test, 20 isolates were resistant which belonged to D (D1 phylogenetic subgroup) and A (A0 phylogenetic subgroup) groups. Conclusion: The results showed that healthy cats could be considered as potential source for the dissemination of ESBL-encoding genes. Further investigations in companion animals and their owners are needed to clarify the importance of spreading of these zoonotic strains.