Staphylococcus aureus is thought to have acquired mecA DNA by horizontal transfer. DNA fingerprints made by restriction nucleases that cut certain sequences of DNA are used to compare complete genomes or particular genes between bacteria. We isolated an epidemic mecA(-) meticillin-susceptible S aureus genotype and, subsequently, a rare isogeneic mecA(+) meticillin-resistant S aureus (MRSA) genotype from a neonate who had never been in contact with MRSA. This MRSA contained mecA DNA that was identical to that in a coagulase-negative staphylococcal strain isolated from this patient, but different from other MRSA genotypes. We believe that this MRSA was formed in vivo by horizontal transfer of the mecA DNA between two staphylococcal species.