Methicillin-resistant Staphylococcus aureus can become resistant to many different classes of antibiotics. Objective: To characterize aminoglycoside and macrolide resistance mechanisms in MRSA strains in relation to antibiotic susceptibility patterns. Materials and methods: We tested 86 MRSA strains using multiplex PCR for detection of genes mecA, aac(6′)-Ie/aph(2″), ant(4′)-Ia, aph(3′)-IIIa, ermA, ermC and msrA. Results: There was a prevalence of msrA (32.5%), ermC (30.2%) and aph(3')-IIIa (61.6%) genes, which are less frequently reported in MRSA. Most msrA genes was detected in PVL positive strains (92.8%) and was associated only with non-MDR strains, while ermC genes were associated with MDR strains. PVL producing strains were characterized by the presence of aph(3′)-IIIa (93.1%) and msrA genes (93.1%), being phenotypically susceptible to clindamycin. Conclusions: Detection of aminoglycoside and macrolide resistance genes allowed us to establish the concordance between genotypic and phenotypic methods and to correlate the presence of certain resistance genes with the type of circulating strain and the production of virulence factors.