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<i>Staphylococcus aureus</i> is an important pathogen responsible for various healthcare- and community-acquired infections. In this study, whole genome sequencing (WGS) was used to genotype <i>S. aureus</i> clinical isolates from two hospitals in Algeria and to characterize their genetic determinants of antimicrobial resistance. Seventeen <i>S. aureus</i> isolates were included in this study. WGS, single-nucleotide polymorphism (SNP)-based phylogenetic analysis, in silico multilocus sequence typing (MLST), <i>spa</i> and staphylococcal cassette chromosome <i>mec</i> (SCC<i>mec</i>) typing and in silico antimicrobial resistance profiling were performed. Phenotypic antibiotic susceptibility testing was performed using the Vitek 2 system and the disk diffusion method. The isolates were separated into sequence types (STs), with ST80 being predominant; five clonal complexes (CCs); four <i>spa</i> types (t044, t127, t368, t386); and two SCC<i>mec</i> types (IVc and IVa). Whole genome analysis revealed the presence of the resistance genes <i>mecA</i>, <i>blaZ</i>, <i>ermC</i>, <i>fusB</i>, <i>fusC</i>, <i>tetK</i>, <i>aph</i>(3′)-IIIa and <i>aad</i>(6) and mutations conferring resistance in the genes <i>parC</i> and <i>fusA</i>. The rate of multidrug resistance (MDR) was 64%. This work provides a high-resolution characterization of methicillin-resistant <i>S. aureus</i> (MRSA) and methicillin-susceptible <i>S. aureus</i> (MSSA) isolates and emphasizes the importance of continuous surveillance to monitor the spread of <i>S. aureus</i> in healthcare settings in the country.