Staphylococcus aureus is a well-known pathogen that causes several serious diseases in humans and animals. As part of the efforts to control this pathogen, a newly isolated bacteriophage, SA12, which specifically targets S. aureus, was characterized, and its genome was completely sequenced. Host range and bacteriophage challenge tests demonstrated its specific and efficient host lysis of S. aureus. The genome of phage SA12 consists of 42,902 bp length double-stranded DNA with 58 predicted ORFs-encoding phage structure, DNA manipulation, packaging, host lysis, and regulation proteins. The characterization and genome study of phage SA12 in this report is useful for understanding S. aureus-targeting bacteriophages and provides basic information for the further development of phage-based biocontrol agents against S. aureus.