TheKingellagenus includes two pathogenic species, namelyK. kingaeandK. negevensis, as well as strictly commensal species. BothK. kingaeandK. negevensissecrete a toxin called RtxA that is absent in the commensal species. Phylogenetic analysis demonstrates that the toxin-encoding operonrtxCrtxAtolCwas acquired by a common ancestor of the pathogenicKingellaspecies and that a preexisting type I secretion system was co-opted for toxin export. Subsequent genomic reorganization distributed the toxin machinery across two loci, with 30-35% ofK. kingaestrains containing two copies of thertxAtoxin gene. ThertxAduplication is largely clonal and strongly associated with invasive disease. In assays with isogenic strains, a single copy ofrtxAwas associated with reduced virulence in vitro. This study establishes the critical steps in the evolutionary transition from commensal to pathogen, including horizontal gene transfer, co-option of an existing secretion system, and gene duplication.