We investigated the evolutionary history of one MRSA clone (clonal complex CC5) by mutation discovery at 108 loci (46 kb) within a global collection of S. aureus isolates. The single nucleotide polymorphisms that were ascertained define a radial phylogenetic structure within CC5, consisting af several geographically associated clades. By mapping the number of independent imports of the SCCmec methicillin-resistance island, we show that import has occurred much more frequently than previously appreciated and that the progeny of such recombinant strains are usually distributed locally rather than globally. Phylogeographic patterning represented by the core genome was compared to fine-scale variability of SCCmec elements.