The phyllosphere is a rich and varied microbial community comprising organisms with diverse functional types. Its composition is strongly influenced by both genotypic and environmental factors, many of which can be manipulated by breeding, agronomy and crop protection strategies in an agricultural context. These factors also affect the complex interactions between the microbes, which in turn affect their interaction with their host plant. Whether or not an organism becomes pathogenic and the subsequent expression of disease are also influenced by all these factors. Understanding the population dynamic balance between the organisms of the phyllosphere as an ecological system should lead to new approaches in agronomy, crop protection and breeding that enhance sustainability, where the previously presumed requirement to eliminate putative pathogens is replaced by management that favours dominance of beneficial organisms and contains putative pathogens in asymptomatic or stable states.