In this paper, the optimal design of the numbers and positions of actuators in actively controlled structures is formulated as a three-level optimal design problem. Features of this design problem such as discreteness, multi-modality and hierarchical structure are discussed. A two-level genetic algorithm (TLGA) is proposed for solving this problem. The concept, principle and solution process of the TLGA are described. A case study is presented, in which a building is subjected to earthquake excitation and controlled by active tendon actuators. The results of this study show that: (1) the design problem for optimizing number and configuration of actuators simultaneously in actively controlled structures has the features of non-linearity, mixed-discreteness and multi-modality; (2) a three-level design model can give a reasonable description for this kind of design problem; (3) TLGA is an effective algorithm for solving the combinatorial optimization problem.