Multiple rRNA operons in bacteria can facilitate homologous recombination of both horizontally acquired and genomic DNA (Lan & Reeves, 1998; Sato & Miyazaki, 2017). Indeed, homologous recombination between rRNA operons can cause large genomic rearrangements in Salmonella (Helm et al., 2003; Liu & Sanderson, 1998) and E. coli (Hill & Harnish, 1981). Here we show that Staphylococcus aureus rRNA operons also facilitate homologous recombination and that this can promote a novel route of phage mediated transduction, here called recombined transduction. Transduction is the process whereby bacterial DNA is packaged and transferred between cells by phages (Ning et al., 2019). Here we show that large DNA circles formed by homologous recombination of two neighbouring rRNA operons flanking a prophage can be packaged by the phage when induced, leading to recombined transduction at a higher rate than the basal level of generalised transduction. Furthermore, this phenomenon seems to occur more widely, with similarly structured sequences identified in Salmonella. Our results further blur the lines between the core genome and mobile genetic elements and establishes another form of phage mediated transduction, recombined transduction.