Plant diseases hinder food production globally. Of the known crop plant pathogens, fungi are perhaps the most widely adapted organisms. For disease control, host resistance has been the main method used through major gene deployment. Equally important, has been the use of fungicides. Over the last two decades these two control strategies have been fraught with rapid resistance erosion commonly referred to as the “boom and burst cycle,”. This raises urgent concerns with regard to development of effective alternative strategies such as use of fungicides. The use of fungicides is an effective strategy but they are potential sources of pollution into the environment, pose serious health risks to humans and are uneconomical for low-resource farmers. In this article the potential of how improved disease management strategies embodied in integrated disease management (IDM) can be developed based on a clear understanding of the pathosystem is discussed. We demonstrate that population and molecular genetics can be used to define pathosystems, estimate the evolutionary responsiveness of pathogens and from the data, design appropriate durable control methods. Various population and molecular genetic methodologies are described and how they can be incorporated into standard pathogen characterisation studies. Using grey leaf spot of maize ( Cercospora zeae-maydis
) as a case study, we show how these techniques can be used to generate information on genetic variability, providing for logical development of a durable IDM programme.