Summary Cystic fibrosis (CF) is a genetic disease that results in persistent and chronic lung infections which reduce lung function over time. Pseudomonas aeruginosa (Pa), an opportunistic bacterial pathogen that infects patients lungs at a young age and persists throughout life, is a major contributing factor. Aggressive antibiotic regimes have significantly prolonged the lives of CF patients, yet Pa populations still dominate during end stage lung disease. Why antibiotic treatments against Pa ultimately fail remains unclear, but one plausible explanation is that Pa populations in the CF lung gain higher levels of AMR collectively as they become more phenotypically and genetically diverse over time. Understanding how Pa population heterogeneity contributes to antimicrobial resistance (AMR), and how Pa population diversity contributes to the organism’s survival, are important considerations for the future development of effective diagnostic and treatment strategies. Understanding of in vivo AMR is limited by a lack of empirical studies focused on how factors such as evolutionary trade-offs and social interactions between Pa isolates affect heterogeneity and influence AMR. This study will focus on the impact of intra-species diversity on AMR using a unique set of Pa strain populations already collected from 50 sputum samples. The main goals are to (i) reveal how the level of heterogeneity in Pa populations in CF patients determines the extent of AMR; (ii) ascertain evolutionary factors that leads to AMR heterogeneity; (iii) identify in vivo genomic signatures of AMR using Genome Wide Association Studies (GWAS). The research described in this project will provide valuable insights into antimicrobial resistance in chronic CF infection, because it will introduce novel methodology for antimicrobial susceptibility testing in clinics by taking population dynamics into account. Outcomes could also lead to new models and platforms for studying the evolution of virulence and AMR in populations. In the future, the ideas presented here can be further expanded to include studies on other species important in CF and other polymicrobial communities.