Abstract
Compartmentalisation is a new tool for disease management within a country. In aquaculture, the successful application of compartmentalisation is largely dependent on the system of production and the epidemiology of the disease(s) for which the compartment is being defined. Therefore, compartmentalisation may not be universally applicable across all systems and diseases. The paper examines the implementation of the concept, providing examples of specific industries, and discusses the application of hazard analysis and critical control points (HACCP) to the biosecurity of the system. The role of compartmentalisation in the management of aquaculture disease emergencies is also discussed.