The rate of fluoroquinolone (FQ) resistance among the cephalosporin-resistant Klebsiella pneumoniae is considerably high, however, their genetic profiles have not been well investigated. We selected 61 ciprofloxacin-nonsusceptible isolates from 102 K. pneumoniae isolates judged to be “resistant” to some cephalosporins during 2009 and 2012 throughout Japan. Pulsed-field gel electrophoresis excluded clonal isolates, and 29 isolates were subjected to multilocus sequence typing (MLST), detection of the amino acid substitutions in the quinolone resistance determining regions (QRDRs) of GyrA and ParC, β-lactamase typing, and identification of plasmid-mediated quinolone resistance (PMQR) genes. PCR-based replicon typing was performed, after PMQR gene transfer. Four major sequence types (STs) or clonal complexes (CCs), that is, ST37, CC17 (consisting of ST17 and ST20), ST11, and CC528 (consisting of ST528 and ST1130), were found, and they accounted for 48.2% of the isolates tested. Amino acid substitutions in the QRDRs and the presence of PMQR genes were identified in 20 (68.9%) and 18 (62.0%) isolates, respectively. The replicon type of three PMQR-carrying plasmids was IncN, but others were nontypable. Fifteen (83.3%) of the 18 PMQR-harboring isolates coharbored bla CTX-M and/or bla DHA-1 . Ciprofloxacin-nonsusceptible K. pneumoniae clinical isolates demonstrating cephalosporin resistance often belong to the global epidemic lineages and possess PMQR and/or QRDR substitutions.