Burkholderia pseudomallei (Bp), the causative agent of melioidosis, is an opportunistic environmental bacterium found in tropical regions worldwide. Melioidosis has many different presentations, the most common being pneumonia. Bp generally causes acute disease but may give rise to chronic infection especially in patients with cystic fibrosis (CF), a hereditary disease that leads to impaired clearance of microorganisms from the lungs. People with CF have increased risk of developing chronic infection, although the molecular mechanisms behind this presentation are not well understood. This project has comprehensively characterised Bp evolution in chronically infected CF patients using genomics and transcriptomics. Sequential Bp isolates from five CF patients with chronic melioidosis were analysed. Convergent evolution with other chronic CF pathogens was observed, including development of multi-antibiotic resistance, reductive evolution, metabolic adaptation, and virulence factor attenuation. This study identified the first Bp isolates with hypermutator phenotype due to non-functional MutS. We also uncovered two new potential resistance mechanisms towards two clinically relevant antibiotics used in melioidosis treatment, and identified multidrug resistance in three of five cases, a concern for both patient treatment and biosafety. Transcriptomic analysis of isolate pairs grown in artificial sputum media to mimic the CF lung conditions showed differential expression of genes in four of the isolate pairs, and confirmed the role of key genetic mutations in altering gene expression of certain pathways. These findings have provided the first glimpse into the pathogenesis of chronic Bp infections in CF, with important implications for potentially new targeted therapeutic treatment of this recalcitrant pathogen.