The use of genotyping in the epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) is reviewed, with special emphasis on a new method that enables us to track the evolutionary path of each MRSA isolate. The MRSA genome is made up of 2 components: one, mec DNA; and the other, the methicillinsensitive Staphylococcus aureus (MSSA) chromosome to which the mec DNA has integrated. Therefore, the MRSA clonotype can be defined if we know the mec DNA and the type of MSSA chromosome that served as a recipient of the mec DNA. There are 3 types of mec DNA, and various types exist in the MSSA chromosome, which can be detected by ribotyping. Thus, by combined use of mec DNA typing and ribotyping we can describe the MRSA genotype, which should reflect the ancestral MRSA clonotype. We cannot identify the clonotype by analyzing ribotypes of recent MRSA isolates, because the clonotype is defined only by the ribotype of the first MRSA clone from which the recent MRSA strains have derived. After the first MRSA clone emerged, its ribotype would have changed and diversified with time. Through careful analysis of the MRSA genotypes of recent strains, we can infer MRSA clonotypes. Each MRSA genotype can be further divided into subtypes by determining mecl gene polymorphism. The description of the MRSA genotype and subtype of an MRSA strain confers a biologic and genetic basis to the epidemiology of MRSA, since it reflects the evolutionary makeup of the strain.