26Staphylococcus epidermidis is the most commonly isolated species from human skin and the 27 second leading cause of bloodstream infections. Here, we performed a large-scale 28 comparative study without any pre-assigned reference to identify genomic determinants 29 associated with their diversity and adaptation as a "double-side spy", a skin dominant 30 colonization, and a successful pathogen. The pan-genome of S. epidermidis is open with 435 31 core proteins and a pan-genome size of 8034 proteins. Genome-wide phylogenetic tree shows 32 that whole genome sequence is a powerful tool to analyze the complex evolutionary process 33 of S. epidermidis and investigate the source of infection. Comparative genome analyses 34 demonstrate the high diversity of antimicrobial resistances, especially mobile genetic 35 elements. The complicated relationships of host-bacterium and bacterium-bacterium help S. 36 epidermidis to play a vital role in balancing the epithelial microflora. The highly variable and 37 dynamic nature of the S. epidermidis genome may be the result of its success in adapting to 38 broad habitats, which is necessary to deal with complex environments. This study gives the 39 general landscape of S. epidermidis pan-genome and provides valuable insights into 40 mechanisms for genome evolution and lifestyle adaptation of this ecologically flexible 41 species. 42 43 44