Background Staphylococcus aureus is a Gram-positive coccus that colonises or infects humans and a wide range of domestic and wild animals. Various lineages of S. aureus are adapted to ruminants, including cattle, where they commonly cause mastitis. This is of significant animal welfare and economic relevance. Clonal complex (CC) 97 is one of the S. aureus lineages found predominantly in bovines, but also in other animals and humans. Sequence Type (ST) 71 is a related bovine-associated lineage with part of its genome identical to CC97. Thus, it has been assumed that ST71 was a chimera consisting of a fragment of DNA from an unknown donor strain inserted into a CC97 backbone genome. Results In this study, S. aureus ST3042 was identified as a putative donor of this fragment based on core genome multilocus sequence typing and alignment of core and genomic island markers. We also identified a second ST71 lineage from Sardinia that differs from previously known ST71 from Ireland, the United Kingdom and continental Europe, both in size and demarcations of the ST3042-derived insert. Sardinian ST71 sequences also differed from other ST71 in the orientation of a large part of the genome. As the inversion affected the ST3042-derived region, this event must have taken place later in time than the recombination of CC97 and ST3042. Conclusions The observation that ST71 emerged twice adds to the body of evidence that recombination involving large segments of the genome is another, highly effective, mode of horizontal gene transfer in S. aureus and likely contributes to the extraordinary success of this pathogen.