Ecosystem models are one way of implementing an integrated approach to the recovery of heavily depleted systems like those on and over seamounts. We review the three main types of ecosystem models that have been applied in understanding seamounts, their ecology and fisheries; we describe Ecopath-with-Ecosim food web simulation models, agent-based models, and a more complex biogeochemical spatially explicit model (Atlantis). We discuss their capabilities, limitations, uncertainty, advantages and disadvantages, and present some examples. Ecosystem models of seamounts enable us to evaluate true fisheries sustainability in an ecosystem context and analyse alternative management scenarios for seamount ecosystems.