'Staphylococcus aureus' is next to 'Pseudomonas aeruginosa' the most isolated pathogen from the airways of cystic fibrosis (CF) patients, who are often infected by a dominant 'S. aureus' clone for extended periods. To be able to persist, the pathogen has to adapt to the hostile niche of the airways to counteract host defence, antibiotic therapy and the competition with coinfecting pathogens. 'S. aureus' is equipped with many virulence factors including adhesins, toxins that are localized on the chromosome, on plasmids or are phage-related. 'S. aureus' is especially versatile and adaptation and evolution of the pathogen occurs by the acquisition of new genes by horizontal gene transfer (HGT), changes in nucleotides (single nucleotide variations, SNVs) that can cause a selective advantage for the bacteria and become fixed in subpopulations. Methicillin-resistant 'S. aureus' are a special threat to CF patients due to the more severe lung disease occurring in infected patients. Today, with decreasing costs for sequencing, more and more studies using 'S. aureus' isolates cultured from CF patients are being published, which use whole genome sequencing (WGS), multilocus sequence typing (MLST) or spa-sequence typing ('spa'-typing) to follow the population dynamics of 'S. aureus', elucidate the underlying mechanisms of phenotypic variants, newly acquired resistance or adaptation to the host response in this particular niche. In the first part of this review, an introduction to the genetic make-up and the pathogenesis of 'S. aureus' with respect to CF is provided. The second part presents an overview of recent studies and their findings using genotypic methods such as single or multilocus sequencing and whole genome sequencing, which identify factors contributing to the adaptation of 'S. aureus' and its evolution in the airways of individuals with CF.