Genomics have become crucial in addressing the public health challenges posed by antimicrobial resistance (AMR). In this study, we performed the first whole-genome sequencing (WGS) and genomic analyses of clinical Acinetobacter baumannii (A. baumannii) strains isolated at the Sylvanus Olympio University Teaching Hospital in Lomé, Togo. This prospective study, conducted from April 19 to September 02, 2019. Susceptibility profiles were obtained using the Kirby-Bauer disc diffusion method, and the nine studied carbapenem-resistant A. baumannii strains were subjected to next generation sequencing (NGS) using an Illumina platform. All isolates exhibited resistance to imipenem, ticarcillin, clavulanic acid, cefotaxime, and ciprofloxacin, but remained susceptible to colistin, tigecycline, and rifampicin. The study identified five A. baumannii ST1 strains, two ST103 strains, one ST52 strain, and one ST1153 strain. The number of AMR genes per strain ranged from six to 24, whereas the number of virulence genes per strain varied from 32 to 67. Each isolate contained at least one plasmid, with the number of plasmids per isolate ranging from one to four per isolate. The carbapenemase-producing genes blaOXA-23, blaOXA-58, blaOXA-68, blaOXA-69, blaOXA-70, blaOXA-91, and blaNDM-1 were identified, along with blaCTX-M-15 and other antibiotic resistance genes. Additionally, multidrug efflux system genes, including adeCFGHIJKLMNS, abeSJ, and amvA, and a wide array of virulence and biofilm-forming genetic determinants were found in all isolates. Eleven integrons were detected, featuring aac(3)-Ia, sat-2, and dfrA1 cassettes. Tn6018, carrying the mercury resistance gene merR and czcD (Co/Zn/Cd efflux system), and Tn2007, carrying blaOXA-23, were present in six genomes. Four Ghanaian genomes were most closely related to the A. baumannii ST1 and ST103 strains reported in this study. Furthermore, several multidrug resistance plasmids and one virulence and AMR hybrid plasmid (accession number JBFMWK020002174.1) were identified. This study provides valuable insights into clinical A. baumannii in Togo, underscoring the need for more frequent genomic studies in sub-Saharan countries to effectively monitor and combat AMR in Africa.