Marine ecosystem models are reasonably proficient at simulating physically-driven features such as spring blooms. However, the demands on these models are shifting to complex biological issues such as functional diversity, and changes in ecosystems and their services such as exploited fish stocks and carbon sequestration. Current ecosystem models generally use a food web structure reduced to its bare essentials. A consequence of the simplified structure is that they are specialized to a particular time, place and ecosystem state and thereby have limited ability to evolve into a substantially different state as a result of internal dynamics or changes in external forcing. We use food web theory and the ideas from complexity theory to argue that an improved representation of the structure of marine food webs is essential for the next generation of marine ecosystem models. Here we propose that a useful guiding principle for model design is provided by earth system models of intermediate complexity; a willingness to sacrifice process detail in order to increase the number of interacting components in the system and simulate the web of feedback loops.