Enterobacter cloacae complex (ECC) members and Klebsiella aerogenes are Gram-negative, rod-shaped, opportunistic pathogens that cause healthcare-associated infections and significantly threaten immunocompromised patients. Despite their clinical importance, their resistant profile and pathogenicity are not well understood due to the scarcity of studies in Lebanon and worldwide. This study presents a comprehensive whole-genome-based characterization of multidrug resistant and hypervirulent ECC members recovered from clinical settings in Lebanon. Identification and classification of 21 Enterobacter species and three K. aerogenes, was performed through hsp60 genotyping and 16S rRNA gene sequencing and confirmed by whole-genome average nucleotide identity (wgANI). Enterobacter spp. (N=21) were divided into three different genetic clusters: cluster VIII, cluster VI and only one members facilitated the exchange of resistance determinants. Co-selection of resistance and virulence characteristics could have provided a selective advantage. This study confirmed the polyphyletic nature of ECC members and their potential to rapidly evolve and adapt through horizontal gene transfer (HGT). It also revealed the need to expand prevention measures, showed the importance of developing and maintaining surveillance practices to control the spread of these pathogens, and the inevitability of implementing strict infection control measures in healthcare facilities. mapping to cluster XI. Multi-locus sequence typing (MLST) was used to determine the clonality of the isolates and core-genome single nucleotide polymorphism (SNP) to study the phylogenetic relatedness. MLST typing revealed the clonal diversity and helped in identifying epidemic clones such as ST114. Antibiotic susceptibility testing showed that most isolates were extensively drug-resistant (XDR), and the majority resistant to carbapenems(n=22/24). in silico analysis and plasmid-based replicon typing (PBRT) confirmed that the horizontal gene transfer of conjugative plasmids among ECC members facilitated the exchange of resistance determinants. Co-selection of resistance and virulence characteristics could have provided a selective advantage. This study confirmed the polyphyletic nature of ECC members and their potential to rapidly evolve and adapt through horizontal gene transfer (HGT). It also revealed the need to expand prevention measures, showed the importance of developing and maintaining surveillance practices to control the spread of these pathogens, and the inevitability of implementing strict infection control measures in healthcare facilities.