Methods to assure the health of crops owe their efficacy to the extent to which we understand the ecology and biology of environmental microorganisms and the conditions under which their interactions with plants lead to losses in crop quality or yield. But in the pursuit of this knowledge, notions of the ecology of plant pathogenic microorganisms have been reduced to a plant-centric and agro-centric focus. With increasing global change, i.e. changes that encompass not only the climate but also biodiversity, geographic distribution of biomes, human demographic and socio-economic adaptations and land use, new plant health problems will emerge via a range of processes influenced by these changes. Hence, knowledge of the ecology of plant pathogens will play an increasingly important role in anticipating and responding to disease emergence. Here we present our opinion about the major challenges facing the study of the ecology of plant pathogenic bacteria. We argue that the discovery of markedly novel insights into the ecology of plant pathogenic bacteria is most likely to happen in a framework of more extensive scales of space, time and biotic interactions than those that currently guide much of the research on these bacteria. This will set a context that is more propitious for discovery of unsuspected drivers of survival and diversification of plant pathogenic bacteria, of the factors most critical for disease emergence, and will set the foundation for new approaches to sustainable management of plant health. We describe the contextual background, justification for, and specific research questions for the following challenges.