Variation within agro-ecosystems is a universal but complex phenomenon which is present in each of the factors that determine the agro-ecosystem, i.e. the environment, genetic resources and management. Agrodiversity is defined as the variation resulting from the interaction between these factors. This variation manifests itself in many different forms, at different scales and levels of aggregation. Examples show that poor management of agrodiversity in high and low external input agriculture reduces output, output stability, resource-use efficiency and the production potential of the natural resource base. A better understanding of agrodiversity is required to improve its management. Also, analysis of variation in agro-ecosystems requires other approaches in research to be further developed in order to characterize, measure and understand relevant variation.