The increasing use of chlorhexidine for methicillin-resistant Staphylococcus aureus (MRSA) decolonization has raised concerns about the emergence of resistance to or tolerance of this antiseptic. We examined the frequency and characteristics of qacA/B chlorhexidine tolerance genes among MRSA isolates in a surgical intensive care unit (ICU) where MRSA-colonized patients are decolonized by chlorhexidine bathing. The MRSA isolates were evaluated for chlorhexidine susceptibility, mupirocin resistance, molecular typing, agr functionality, and the heterogeneous vancomycin-intermediate S. aureus (hVISA) phenotype according to the presence of the qacA/B genes. Overall, 119 MRSA isolates were obtained from active surveillance cultures (93, 78.2%) and clinical cultures (26, 21.8%) between 2012 and 2014. Among these isolates, 39 (32.8%) carried the qacA/B genes, and 23 (19.3%) exhibited mupirocin resistance. Most qacA/B-positive isolates (36/39, 92.3%) were identified as ST5-SCCmecII (69.2%) and ST239-SCCmecIII (23.1%), which are common healthcare-associated (HA)-MRSA strains in Korea. Multivariate analysis found that qacA/B-positive MRSA isolates were associated with agr dysfunction (OR, 4.87; 95% CI, 1.71-13.87) and the hVISA phenotype (OR, 4.09; 95% CI, 1.48-11.34). In conclusion, our study showed that qacA/B carriage was common among MRSA isolates in an ICU where chlorhexidine is commonly used for decolonization. qacA/B carriage was significantly associated with agr dysfunction and the hVISA phenotype. These features may confer a selective advantage on HA-MRSA strains, including ST5-SCCmecII and ST239-SCCmecIII, in the ICU setting.