CotSim is a size-structured metapopulation model of the crown-of-thorns (Acanthaster planci) on the central Great Barrier Reef (GBR). The populations of starfish and the coral cover on 269 individual reefs are modelled for up to 200 years. Starfish are represented as larvae, two age classes of juveniles and three size classes of adults. Coral can either be modelled as a single type or as two types each with a characteristic growth rate, equilibrium cover and susceptibility to starfish predation. Reefs are connected using simulated dispersal data for A. planci on the central GBR. These data were generated using a particle tracking program where simulated currents displaced particles representing dispersing larvae after an A. planci spawning episode. The dispersal data represented patterns expected from the 1976/77 to 1989/90 spawning season. The starfish growth model is a density-dependent matrix model. When coral cover is low, survival within classes is low and the transitions into larger classes is impeded. In contrast, at high coral cover the reverse patterns occur. Both the starfish and coral data are filtered through an interpretation model to generate observed patterns. The starfish interpretation model represents the important difficulty in detecting smaller adults. Results from the model using the default parameters correspond with published patterns of starfish/coral dynamics and the overall patterns of starfish outbreaks on the GBR.The model is an interactive event-driven 32-bit Windows application requiring Windows 95 or Windows NT 3.51/4.0. Most parameters are able to be altered by the user with three tabbed dialogue boxes (for the simulation, starfish and coral parameters). Biologically justifiable default parameters are provided for all parameters. Parameters and initial starfish populations are stored in simple coded ASCII files. Simulations are controlled using 'Run', 'Pause/Continue' and 'Stop' operations. Maps of the GBR illustrate the spatial and temporal structure of the metapopulation dynamics including the patterns of dispersal. Once paused, populations on individual reefs can be examined using two types of plots (time series and single time bar charts). Overall patterns can be displayed using latitude versus time plots of observed reef state. Starfish populations and coral cover can be edited, which enables users of the model to become associated with some of the key issues regarding large-scale starfish control programs. Results from the model can be written to ASCII files for additional analysis. The speed of a simulation is able to be controlled and colours for important graphical elements can be altered. CotSim includes indexed online context-sensitive help and a graphical install routine. The program adheres to published guidelines for Windows applications.