Epidemic methicillin-resistant Staphylococcus aureus types 15 and 16 (EMRSA-15 and EMRSA-16) are the dominant types of MRSA found in UK hospitals, but accurate designation of strains has been difficult. Restriction fragment length polymorphism (RFLP) profiles of seven core virulence genes were used to classify unambiguously isolates of MRSA from St George's Hospital into two groups corresponding to EMRSA-15 and EMRSA-16. Variants of both EMRSA-15 and EMRSA-16 isolates occurred that had lost virulence genes encoded on mobile genetic elements. EMRSA-16 isolates had core gene profiles identical to a cluster of previously characterised MSSA (methicillin-sensitive S. aureus) isolates from St George's Hospital, suggesting that they have arisen from this source, or that loss of the accessory genetic element encoding methicillin resistance is frequent. EMRSA-15 and EMRSA-16 strains were distinct from other MRSA strains previously identified in UK hospitals, and always carried a mobile genetic element encoding multiple superantigens. These results contribute to the understanding of the types of MRSA found in UK hospitals, how they vary and how they arose.