We studied the usefulness of the restriction-modification (RM) test, staphylococcal cassette chromosome (SCC) mec types, and Panton-Valentine leukocidin (PVL)-encoding phages to identify Staphylococcus aureus methicillin-resistant lineages and to differentiate clones that belong to the same lineage. A total of 108 methicillin-resistant S. aureus (MRSA) strains were characterized by pulsed-field gel electrophoresis (PFGE)--multi-locus sequence typing (MLST)--spa-typing. The RM correctly identified the lineages CC5, CC8, CC30, and CC398, but not CC25 and CC72. The SCCmec and RM combined analysis allowed differentiation between MLST types within the same lineage. Only 5 MRSA strains were PVL-positive. Four PVL-positive USA300 isolates carried elongated-head type PVL-encoding phages, while the sequence type (ST)-30 strain carried an icosahedral-head phage. The combination of the RM test method, SCCmec types, and PVL phage identification could be useful for MRSA typing purposes.