A cybernetic technology of mechatronic design of active magnetic bearings systems (AMB) originated from theory of systems is suggested in the paper. Traditional models of artificial intelligence and mathematics do not allow describing mechatronic systems being designed on all its levels in one common formal basis. They do not describe the systems structure (the set of dynamic subsystems with their interactions), their control units, and do not treat them as dynamic objects operating in some environment. They do not describe the environment structure either. Therefore, the coordination technology of hierarchical systems has been chosen as a theoretical means for realization of design and control. The theoretical basis of the given coordination technology is briefly considered. An example of technology realization in conceptual and detailed design of AMB system is also presented.