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Carbapenem and colistin-resistant bacteria represent a global public health problem. Refugees carrying these bacteria and living in inadequate shelters can spread these microorganisms. The aim of this study was to investigate the intestinal carriage of these bacteria in Syrian refugees in Lebanon. Between June and July 2019, 250 rectal swabs were collected from two refugee camps in North Lebanon. Swabs were cultured on different selective media. Antibiotic susceptibility testing was performed using the disk diffusion method. Carbapenemase-encoding genes and <i>mcr</i> genes were investigated using real-time polymerase chain reaction (RT-PCR) and standard polymerase chain reaction (PCR). Epidemiological relatedness was studied using multilocus sequence typing (MLST). From 250 rectal swabs, 16 carbapenem-resistant, 5 colistin-resistant, and 4 colistin and carbapenem-resistant <i>Enterobacteriaceae</i> were isolated. The isolates exhibited multidrug-resistant phenotypes. Seven <i>Klebsiella pneumoniae</i> isolates harboured the <i>bla</i>_OXA-48 gene, and in addition four <i>K. pneumoniae</i> had mutations in the two component systems pmrA/pmrB, phoP/phoQ and co-harboured the <i>bla</i>_NDM-1 gene. Moreover, the <i>bla</i>_NDM-1 gene was detected in six <i>Escherichia coli</i> and three <i>Enterobacter cloacae</i> isolates. The remaining five <i>E. coli</i> isolates harboured the <i>mcr-1</i> gene. MLST results showed several sequence types, with a remarkable clonal dissemination. An urgent strategy needs to be adopted in order to avoid the spread of such resistance in highly crowded underserved communities.