Presence of methicillin-resistant Staphylococcus aureus (MRSA) strains carrying plasmid-borne multidrug efflux pump-encoding gene, qacA/B , is a serious issue for infection control in hospitals, because they can survive hand hygiene. The qacA/B genes are divided into five subtypes: qacA , qacBI , qacBII , qacBIII , and qacBIV . The aim of this study was to investigate the prevalence and risk factors of hospitalized patients infected by respective qacA/B -positive MRSA strains between 2010 and 2016 in Tokyo, Japan. Of the 600 total MRSA strains observed, the qacA/B -positive strains constituted 19.8% (199 isolates), of which 56.8% (113 isolates), 28.6% (57 isolates), and 14.6% (29 isolates) were classified as qacA , qacBIII , and qacBII -positive strains, respectively. The prevalence of qacA -positive MRSA strains significantly decreased from July 2010 to June 2011 (34.0%) to July 2015 to May 2016 (5.3%) ( p < 0.05). When staphylococcal cassette chromosome (SCC) mec types of the respective qacA/B -positive strains were determined, 81.4% of the qacA -positive strains were classified into SCC mec type II, which has recently been decreasing in hospital-acquired MRSA in Japan. Risk factor analysis showed that there were no specific clinical departments associated with the presence of qacA -positive strains. Our findings suggest that change in the MRSA clonal lineages impact to decrease the prevalence of qacA -positive strains in Japanese hospitals.