Prophages have important roles in virulence, antibiotic resistance, and genome evolution inStaphylococcus aureus. Rapid growth in the number of sequencedS. aureusgenomes allows for an investigation of prophage sequences at an unprecedented scale. We developed a novel computational pipeline for phage discovery and annotation. We combined PhiSpy, a phage discovery tool, with VGAS and PROKKA, genome annotation tools to detect and analyse prophage sequences in nearly 10 011S.aureusgenomes, discovering thousands of putative prophage sequences with genes encoding virulence factors and antibiotic resistance. To our knowledge, this is the first large-scale application of PhiSpy on a large-scale set of genomes (10 011S.aureus). Determining the presence of virulence and resistance encoding genes in prophage has implications for the potential transfer of these genes/functions to other bacteria via transduction and thus can provide insight into the evolution and spread of these genes/functions between bacterial strains. While the phage we have identified may be known, these phages were not necessarily known or characterized inS. aureusand the clustering and comparison we did for phage based on their gene content is novel. Moreover, the reporting of these genes with theS. aureusgenomes is novel.