This paper is the first attempt of analysing the EU aquaculture sector following a disaggregated approach and including public subsidies within a global CGE modelling framework. Using the MAGNET model, it distinguishes five aquaculture sectors, one wild-captured fish and one fish processing sectors. Furthermore, it adds to the system a fishmeal and fish oil processing sector. Both modelling and data adjustments are needed to properly integrate these new features. This paper pays special attention in the incorporation of cost structures for newly added sectors as well as the representation of income subsidies in aquaculture. It set up a baseline at the horizon 2050, looking how the fish related sectors are expected to develop and what could change if extra EU subsidies would be introduced. It also analyses whether the impact of the aquaculture subsidies could differ substantially if the demand for fish products would develop more rapidly than expected.