An evolutionary algorithm based approach for selection of topologies in hierarchical fuzzy systems (HFS) is presented. Coupling fuzzy system with evolutionary algorithm provides a solution to the automated acquisition of the fuzzy rule base. It is difficult to study the problem of hierarchical decomposition for a large class of fuzzy systems but it is possible to analyse such architectures on the example of a particular fuzzy system, such as inverted pendulum. Topology of the HFS must be selected according to the physical properties of the dynamical system under consideration. Different HFS topologies for an inverted pendulum system are investigated and analysed to address the problem of how input configuration in multi-layered structure affects the controller performance. The experiments are conducted to test controller performance for different topologies of the hierarchical fuzzy system. The impact of different topologies on control process is discussed. The results from the case study of inverted pendulum can be extended to other dynamical systems.