Nowadays, manufacturing control systems can respond more effectively to exigent market requirements and real-time demands. Indeed, they take advantage of changing their structural and behavioural arrangements to tailor the control solution from a diverse set of feasible configurations. However, the challenge of this approach is to determine efficient mechanisms that dynamically optimise the configuration between different architectures. This paper presents a dynamic hybrid control architecture that integrates a switching mechanism to control changes at both structural and behavioural level. The switching mechanism is based on a genetic algorithm and strives to find the most suitable operating mode of the architecture with regard to optimality and reactivity. The proposed approach was tested in a real flexible job shop to demonstrate the applicability and efficiency of including an optimisation algorithm in the switching process of a dynamic hybrid control architecture.