Background: Fluoroquinolones resistance usually occurs due to mutation in the quinolone resistance-determining regions (QRDRs) in the gyrA and parC genes that can be detected by multiplex allele-specific PCR (MAS-PCR). Herbal medicines are used as alternative treatment for disease caused by resistant bacteria. Objectives: This work aimed to detect resistance to fluoroquinolones in E. coli isolates from patient admitted in Mansoura University Hospitals; additionally, to identify certain natural plant extracts that could be used against fluoroquinolone resistant E. coli. Methodology: Fifty clinical E. coli isolates were collected from patients admitted in Mansoura University Hospitals. Fluoroquinolones susceptibility pattern was tested by disk diffusion method. Out of 50 isolates, 25 fluoroquinolone resistant E. coli were selected to detect mutations in gyrA and parC genes by MAS-PCR. Ethanolic plant extracts were tested against FQ resistant E. coli isolates by using agar well diffusion method. Results: E. coli isolates showed highest resistance to ciprofloxacin (76%) followed by norfloxacin (72%), levofloxacin (70%), and ofloxacin (68%). Double mutations at gyrA gene were detected at position 83 and 87 of QRDRs in 12 (48%) FQ resistant E. coli and at parC gene at position 80 and 84 of QRDRs in 3 (12%) FQ resistant E. coli. While single mutation at position 83 and 87 was found in QRDR of gyrA in 8 (32%) and 5 (20%) of FQ-resistant E. coli, respectively and single mutation at position 80 and 84 was found in QRDR of parC in 21 (84%) and 1 (4%) of FQ-resistant E. coli, respectively. Ethanolic extract of Clove had more antibacterial activity compared to other extracts. Conclusion: high rate of fluoroquinolone resistance among clinical E. coli isolates was detected and this necessitates monitoring the microbial trends and resistance patterns. Plants may be used as natural antibiotics in the treatments of antibiotic resistant E. coli infections.