Little work dealing with the evaluation of aquaculture system sustainability has so far been undertaken on a global and comparative basis. Moreover, such work is mostly based on very unbalanced approaches in terms of the dimensions of sustainable development that are taken into account. The approach adopted in this article is designed to encompass all the dimensions of sustainability including the institutional one (governance). The taking into account of this latter, in particular, together with the role played by aquaculture in sustainability at the territorial level gives the approach its original and innovative nature. The process of establishing the checklist of sustainability indicators in aquaculture relies on a hierarchical nesting approach which makes it possible to link indicators with general sustainability criteria and principles. At once multidisciplinary and participatory, the approach compares several countries with highly differentiated types of aquaculture system. An original finding from this work is that the technically most intensive farming model scores better than more extensive systems, which might have been thought to be closer to natural systems in their environmental dimension and therefore intuitively more 'sustainable'. This result suggests relating sustainability outcomes to the level of control and of devolved responsibilities.