To describe the clinical and molecular characteristics of methicillin-resistant Staphylococcus aureus (MRSA) strains that were collected in the Hospital Regional de Alta Especialidad de Veracruz (HRV). A total of 107 MRSA strains from individual patients were examined. The strains were collected between September 2009 and September 2010. The clinical and demographic characteristics of patients were analyzed; molecular typing by pulsed-field gel electrophoresis (PFGE), staphylococcal chromosomal cassette mec (SCCmec) typing and multilocus sequence typing were used to characterize the isolates. Two PFGE patterns (NY/J and IB) were identified with 4 and 3 subtypes respectively. The isolates analyzed showed two SCCmec types (I and II) and two sequence types (ST): ST247 and ST5 related with the Iberian and New York/Japan clones respectively. This study establishes the presence of two very important clonal lineages of MRSA: New York/Japan and Iberian clone in the hospital environment.