As a new rotor control scheme, isotropic control of weakly anisotropic rotor bearing system in complex state space is proposed, which utilizes the concepts on the eigenstructure of the isotropic rotor system. Advantages of the scheme are that the controlled system always retains isotropic eigenstructure, leading to circular whirling due to unbalance and that it is efficient for control of unbalance response. And the system analysis and controller design becomes simple and yet comprehensive since the order of the matrices treated in the complex domain approach is half of that in the real approach. The control scheme is applied to a rigid rotor-active magnetic bearing system which is digitally controlled and the control performance is investigated experimentally in relation to unbalance response and control energy. It is found that the isotropic optimal control method, which essentially eliminates the backward unbalance response component, is more efficient than the conventional optimal control in that it gives smaller major whirl radius and yet it often requires less control effort.