The drug resistance was investigated in swine clinical isolates of Escherichia coli in East China, and the prevalence of plasmid-mediated quinolone resistance (PMQR) genes was detected by PCR and sequencing. Among 53 clinical E. coli isolates, 47 (88.7%) isolates exhibited resistance to one or more antimicrobial agents, with the greatest resistance in norfloxacin (69.8%) and ciprofloxacin (67.9%) and the lowest resistance in amikacin (17.0%). In total, aac(6’)-Ib, qnr and qepA were detected in 10 (18.9%), 10 (18.9%) and 1 (1.9%) of 53 E. coli isolates. The 10 qnr-positive isolates include 5 for qnrB and 5 for qnrS, whereas no qnrA and qnrD were detected. Noteworthy, 90% (9/10) aac(6’)-Ib-positive isolates were the cr variant allele. The fact that, none resistance gene was detected in some isolates with severe drug resistance, suggests that there may be other potential genes or mechanisms mediating it.