Antimicrobial resistance profiles, restriction fragment length polymorphism of the coagulase gene and repetitive element sequence-based PCR were used to classify 210 methicillin-resistant Staphylococcus aureus isolates recovered between 1997 and 2005 in two hospitals in Vigo, north-west Spain. Representative isolates belonging to the epidemic clones were analysed by spa typing and multilocus sequence typing, and the staphylococcal chromosomal cassette (SCC)mec type was determined for all isolates. The New York/Japan clone (t002-ST5-II) was detected in Spain for the first time. However, the New York/Japan and the Brazilian (t037-ST239-IIIA) clones were replaced by EMRSA-16 (t018-ST36-II), which at present is the predominant clone.