The genome sequence of Pectobacterium atrosepticum (Pba), one of the most economically damaging bacterial diseases of potato in temperate regions, was published in 2004. Even though, at the time, the number of completely sequenced bacterial genomes numbered only in the low hundreds we were able to use comparative genomics techniques to identify novel regions of DNA that were specific to Pba or only shared with closely related bacteria. Pba was found to contain many genes that were previously undescribed in this group of pathogens but were potentially coding for pathogenicity determinants, some of which appeared to be involved in either triggering or suppressing the plant’s disease resistance processes. Our work since then has employed functional genomics methods to elucidate the ways in which this pathogen interacts with plants and causes disease, and how it has acquired the means to do this. These studies have allowed us to demonstrate a role in pathogenesis for bacterial genes, and to identify potato genes involved in resistance, leading to production of a transgenic potato plant that was fully resistant to the pathogen. Pba genes involved in phenotypes suited to a plant-associated lifestyle were also identified, with roles including attachment to, and colonization of, the roots of both crops and weeds. This understanding has led us to study alternative host plants for Pba in the environment, and the importance of this mode of environmental persistence for pathogen epidemiology and its spread to and between potato crops. Recently, we sequenced 25 strains representing the species range of the related phytopathogenic Dickeya genus (all formerly Erwinia chrysanthemi). Comparative genomic analyses of these sequences enabled application of a novel bioinformatics pipeline for generating diagnostic primers, enabling assays for the soft rot potato pathogens D. dianthicola and D. solani (which are an increasing problem on potato in Europe) as well as other Dickeya species. These assays are currently being validated for molecular diagnostic testing by a number of European plant health laboratories.