We have previously generated strains of Staphylococcus aureus SA003 resistant to its specific phage ?SA012 through a long-term coevolution experiment. However, the DNA mutations responsible for the phenotypic change of phage resistance are unknown. Whole-genome analysis revealed eight genes that acquired mutations: six point mutations (five missense mutations and one nonsense mutation) and two deletions. Complementation of the phage-resistant strains by the wild-type alleles showed that five genes were linked to phage adsorption of ?SA012, and two mutated host genes were linked to the inhibition of post-adsorption. Unlike ?SA012, infection by ?SA039, a close relative of ?SA012, onto early coevolved phage-resistant SA003 (SA003R2) was impaired drastically. Here, we identified that ?SA012 and ?SA039 adsorb to the cell surface S. aureus SA003 through a different mechanism. ?SA012 requires the backbone of wall teichoic acids (WTA), while ?SA039 requires both backbone and the -GlcNAc residue. In silico analysis of the ?SA039 genome revealed that several proteins in the tail and baseplate region were different from ?SA012. The difference in tail and baseplate proteins might be the factor for specificity difference between ?SA012 and ?SA039.