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The emergence of extended-spectrum cephalosporin (ESC)-resistant Gram-negative bacteria is of great concern in both human and veterinary medicine. The aim of this study was to investigate ESC-resistant bacterial isolates from companion animals in South Korea between 2017 and 2019. Isolates with ESC resistance genes, which were identified by PCR, were assessed for genetic relatedness by multi-locus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). In total, 91 ESC-resistant <i>Escherichia coli, Klebsiella</i> spp., <i>Serratia</i> spp., and <i>Enterobacter cloacae</i> isolates harbored the <i>bla</i>_TEM gene. Among other ESC resistance genes, <i>bla</i>_CTX-M-15, <i>bla</i>_CIT, and <i>bla</i>_CTX-M-55 were predominantly detected in <i>E. coli</i> isolates, whereas <i>bla</i>_SHV and <i>bla</i>_DHA were more frequently detected in <i>Klebsiella pneumoniae</i> isolates. In addition, all <i>bla</i>_EBC-positive isolates were classified as <i>E. cloacae</i>. From the MLST results, <i>bla</i>_CTX-M-9-carrying ST131, <i>bla</i>_CIT-carrying ST405, and <i>bla</i>_CTX-M-1-carrying ST3285 strains were dominant among <i>E. coli</i> isolates. ST273 and ST275 strains harboring <i>bla</i>_SHV were frequently detected in <i>K. pneumoniae</i> isolates. Various sequence types were obtained in <i>E. cloacae</i> and <i>Klebsiella oxytoca</i> isolates. All isolates demonstrated unique PFGE profiles (<57–98% similarity) and were unlikely to be derived from a single clone. The present study reveals the presence and wide genetic distribution of ESC-resistant bacterial species in South Korean companion animals.