Staphylococcus (S.) aureus can harbour many virulence factors and these include leukocidins, which are bi-component toxins encoded by two co expressed genes. Some of these toxin genes are localised on prophages and thus they are potentially transmissible. In many cases, they determine the host specificity of the strain they reside in. One set of leukocidin genes, lukM/lukF-P83, is known to occur in isolates from bovids, small ruminants and rodents. It has also been shown to occur in two lineages of S. aureus from red deer (Cervus elaphus) in Italy. Three deer isolates from two lineages, clonal complexes (CC) 350 and 425, were subjected to genome sequencing applying nanopore technology. In addition, phages were induced by mitomycin C treatment, sequenced and imaged by transmission electron microscopy (TEM). The lukM/lukF-P83 leukocidin genes were situated on a Peeveelvirus prophage that integrated into the A5IU43 = yfkAB gene and that was inducible by mitomycin C. The prophage sequences of CC350 and CC425 were nearly identical. They differed from other, previously published lukM/lukF-P83-prophage sequences with most of which, however, they shared the integration site. In addition, the CC350 isolate harboured another, apparently hybrid prophage which was not inducible. Both CC425 isolates also carried an inducible Triavirus prophage. While various S. aureus lineages have been observed in deer, data on their virulence factors remain insufficient. Our observations should prompt further investigations on cervids, both wild or captive. Red deer in zoo or game park populations, together with post-mortem examinations of free-ranging deer found dead, culled for management or harvested by hunters, should provide ample opportunities to observe animals for skin and soft tissue infections including mastitis which are known to be associated with lukM/lukF-P83 in other animals.