This paper focuses on the design of a controller for a low temperature ethanol steam reformer for the production of hydrogen to feed a Protonic Exchange Membrane (PEM) fuel cell. It describes different control structures for the reformer and treats the control structure selection of this Multiple Input Multiple Output (MIMO) system. For each control structure, decentralised 2x2 controllers are implemented and a Proportional Integral (PI) control action is implemented in each control loop. The PI parameters are tuned and the performance of the different linear controllers is compared though simulation. For the evaluation of the proposed controllers, the response time for different initial conditions and changes in the references is analysed, as well as the behaviour of the controlled system in front of disturbances.