This study aimed to describe the prevalence and the characterization of resistance mechanisms of ciprofloxacin resistant Escherichia coli isolated from food and patients in China.Methods Ciprofloxacin resistant Escherichia coli isolates were selected from 645 isolates in ciprofloxacin containing plates. Antimicrobial susceptibility testing, phylogenetic analysis, quinolone and blaCTX-M resistance mechanisms were detected by polymerase chain reaction and sequencing were carried out. Results Totally, twenty one (3.3%) ciprofloxacin resistant Escherichia coli isolates were identified. Point mutations in topoisomerase encoded genes gyrA, parC and parE were confirmed, and all isolates carried plasmid-mediated quinolone resistance genes (PMQR), including oqxA, oqxB, qnrS, aac(6′)-Ib-cr and qepA but qnrA, qnrB, qnrC and qnrD were not detected. All 21 ciprofloxacin resistant isolates also harbored blaCTX-M genes.Conclusion The isolates from food and patients showed complicated and diverse quinolone resistance mechanisms and the possible transmission of PMQR may pose potential risk to public health. In order to investigate aspects of transmission between food and community-acquired strains and to provide a scientific basis for humans, the continuous surveillance of multidrug-resistant Escherichia coli should be carried out.