Models are tools that aid managers to make decisions in a transparent manner. Models are implicitly used to devise any management plan, but scientific modelling makes the approach explicit and transparent. Simple models are often more useful than complex models, especially when time and data are short--as in many emergency situations. Four areas in which modelling can help aquatic animal health managers to control or prevent disease emergencies are identified, and their application reviewed. These areas are: models of factors behind disease outbreaks; models for the design of efficient surveillance; models of disease spread (subdivided into Susceptible-Infected-Removed [SIR] models, coupled hydrodynamic-particle transport models and network models); and models to evaluate the consequences of disease outbreaks. Import risk analysis and SIR modelling have been applied fairly extensively; risk-based surveillance is likely to be a driver for increased modelling effort in the near future.