ST239-MRSA-III is a nosocomial MRSA clone that is frequently isolated throughout the world. It has a hybrid chromosome, which is hypothesized to be the result of a large recombination between two other prevalent MRSA clones. Nearly all ST239 strains carry an SCCmec type III element. PFGE-defined variants of ST239 can exhibit different virulence-associated traits, and different ST239 populations can exhibit different epidemiological dynamics. The goal of this study was to use high resolution sequence-based strain typing and phylogenetic analysis to identify clonal and SCCmec type III variants among ST239, and to elucidate their patterns and mechanisms of evolutionary descent. The study sample consisted of 102 diverse isolates that were collected over a period of 24 years from 28 countries. Clonal variation was studied with 7 MLST genes, 7 SAS genes, and the 2 junctions of ST239's chromosomal recombination. In addition, a novel sequence variation discovery method, called reduced representation shotgun (RRS) sequencing, was used to pinpoint a further 5 polymorphic loci. Partial sequencing of these 21 loci from all isolates revealed 20 composite sequence types. Maximum parsimony analysis generated a single most parsimonious tree, which displayed a Y-shaped topology with 3 prominent lineages. One lineage was most similar to ST239's putative parents, and it contained the oldest available ST239 strain, ANS46, suggesting that this lineage may be ancestral. Surprisingly, the Slatkin-Maddison test, which is an association test between a phylogeny and strain characteristics, revealed a strong (P=0.0079) geographic component to the phylogeny, with predominantly Asian (34/44 isolates), South American (13/24 isolates), and European (16/21 isolates) lineages, corresponding to the 3 prominent lineages. To our knowledge, this is the first phylogeographic pattern described for any staphylococcal clone. SCCmec type III variation was studied with multiplex PCR and partial sequencing of the ccrB and dru loci. Multiplex PCR revealed 9 SCCmec type III variants that were randomly distributed across the phylogeny (P=0.5366). In contrast, ccrB revealed 4 alleles that mapped nonrandomly across the phylogeny (P=0.0026). The dru locus revealed 40 alleles, which was significantly more diverse than the other SCCmec typing tools (P<0.05), and only 1 dru allele was phylogenetically inconsistent. These data indicate that the dru locus provides a diverse, informative marker for characterizing SCCmec type III elements. In summary, this study has resolved portions of the ST239 global phylogeny and identified genetic markers that can be used to begin to unravel the complex epidemiology of this MRSA clone.