Marine foodweb models are important tools for guiding sustainable management decisions and for evaluating the potential combined effects of harvesting and climate change. A key challenge is handling uncertainty in these models to ensure they provide robust predictions and management advice. Uncertainty is arguably highest for parameters relating to mid-trophic levels – in particular mesopelagic fish – for foodweb models in many regions, despite the fact that these groups are thought to play a central role in trophic energy transfer. Stable isotope signatures are an important data source for both parameterising these mid trophic levels, and for evaluating model skill. However the full potential of this data source has not been realised, and the implications of recent theoretical advances in the analysis and interpretation of stable isotope data have not yet been considered. We review the development and evaluation process for ecosystem models and assess the potential for incorporating stable isotope results into the parameterisation and evaluation of these models. This review provides an integrated framework for understanding how stable isotope data are used in both size- and species-based models, and clearly identifies priorities for future work. We conclude by discussing an example - a foodweb model under development for Prydz Bay and the southern Kerguelen Plateau region in the Indian Sector of the Southern Ocean- and consider the implications of our modelling work for evaluating the effects of climate change and fishing in the region.