Management of biological systems involves the application of ecological and evolutionary principles within a decision theory framework. In the present review, we focus on epidemiology and pest (insect and plant) control. By studying their similarities and differences, it is possible to outline a broad conceptual background for the antagonistic interactions involved, and hence to begin to develop a classification system of predictive value in management situations. In particular, we address issues of scale in space and time, and relate these to contrasting practical problems associated with deploying biocontrol agents and disease control. Additionally, we discuss three areas where an integrated approach to natural enemies, using ecological and evolutionary insights, and decision theory have much to offer: (i) management and resistance, (ii) the problems of emerging diseases, and (iii) the links between disease and behaviour.