Pseudomonas aeruginosa is an opportunistic pathogen that can invade and colonise the lungs of people with cystic fibrosis (CF), cause septic shock through bacteraemia infections, and lead to serious infection of burn injuries. It is one of the most critical multi-drug resistant bacteria, and is associated with high morbidity and mortality. A total of 4,094 P. aeruginosa isolates were sampled from nine patients with CF over a six-month time period. These isolates were collected from sputum samples during stable, acute, and recovery timepoints from periods of sudden and rapid lung function decline, called acute pulmonary exacerbations (APEs). These isolates were previously analysed for the presence and absence of ten virulence-related phenotypes. The P. aeruginosa isolates were whole-genome sequenced to investigate the inter- and intra-patient genotypic diversity, associations with phenotypic diversity, and adaptation within the CF lung. Each of the nine patients with CF were colonised with a distinct clone of P. aeruginosa. Six patients were infected with well-characterised, highly-transmissible strains of either the Liverpool Epidemic Strain (LES) or the Manchester Epidemic Strain (MES). The remaining three patients were infected with novel sequence types (STs); ST3307 or ST3308. Putative transmission was identified between the two patients infected with ST3307. Two large deletions in genetic regions commonly associated with progression from acute to chronic infection were identified in ST3307. The acquisition of the LES by one of the patients was very recent, estimated to have occurred within the two years prior to the study. This recent acquisition provides an insight into the immediate adaptation of P. aeruginosa to the CF lung, with adaptation observed in genetic regions associated with progression from acute to chronic P. aeruginosa infection. The timepoints for each APE within the individual patients were not associated with variation in the diversity of the populations of isolates. This was confirmed by random distribution of phylogenetic clusters with respect to each APE timepoint for most patients, suggesting that APEs, and the treatment of APEs, do not substantially affect the diversity of the P. aeruginosa population within the patient lung. Genome-wide association studies (GWAS) were carried out on the CF isolates, to investigate any associations with the ten previously-tested virulence-related phenotypes. Population structure could be effectively controlled for in this highly structured dataset, using linear mixed models. Multiple GWAS approaches were required to capture the different classes of genetic variation, resulting in the identification of biologically relevant associations for complex phenotypes, most notably a premature stop-codon in the global transcriptional regulator rhlR, as well as several novel, potentially significant associations. An additional 352 P. aeruginosa isolates from patients with bacteraemia were also whole-genome sequenced. These isolates were sourced from both a local collection and from a UK-wide surveillance collection, and broadly match the defined population structure of P. aeruginosa. Three STs were overrepresented in this dataset, which are associated with virulence and multi-drug resistance; ST175, ST253 and ST395. One of these overrepresented STs, ST175, was distributed across the UK, shows significant geographical clustering and temporal signal, and is predicted to have been introduced into the UK between the late 1980s and the early 1990s. Antimicrobial resistance profiles showed that current therapeutic options are still viable for most P. aeruginosa bacteraemia infections, and that colistin is still effective against the most multi-drug resistant isolates.