We identified 25 high-level mupirocin-resistant (MuH) and 21 low-level mupirocin-resistant (MuL) Staphylococcus aureus isolates from eight long-term-care facilities (LTCFs). The pulsed-field gel electrophoresis patterns of 19 MuH and 19 MuL isolates from two facilities were identical for 18 and 15 isolates, respectively. The most predominant mupA restriction fragment length polymorphism type was found in 21 MuH isolates. We conclude that clonal transmission of MuH and MuL S. aureus strains occurred in these LTCFs. This is the first report of clonal transfer of mupirocin resistance in LTCFs.