The management of emerging infectious disease outbreaks is a defining problem of our ever more mobile and connected world. Pathogen genomes contain a remarkable amount of information about disease transmission, and genomic technologies are being used increasingly to investigate new outbreaks. Yet the contribution that genomics can make to infectious disease surveillance is only beginning to be appreciated by public health agencies. Professor Oliver Pybus, Co-Director of the Oxford Martin Programme on Pandemic Genomics, will outline the opportunities and challenges ahead as we try to integrate genomic data into epidemic control efforts.