Moraxella catarrhalis is an important bacterial respiratory pathogen. This thesis sought to add to currently limited knowledge of M. catarrhalis genomic structure. High-throughput sequenc ing was used to obtain 86 M. catarrhalis whole genomes. Pan genome analysis revealed cladal differences in nutrient uptake genes and CRISPRs. The diversity of virulence genes was
demonstrated in relation to disease presentation, host age, strain source and cladal structure. Evolutionary modelling revealed unexpected pressures affecting these genes. Thirty-two novel Siphoviridae-related prophages, viral genomes within the bacterial chromososomes, were described, which harboured hyperconserved genes. Epifluorescence microscopy provided the first demonstration of active viruses in M. catarrhalis.