Non-self-adjoint dynamical system commonly appears in rotor dynamics, flutter analysis and control synthesis, where the symmetry of the system matrices are destroyed. The asymmetry of the system matrices leads to challenges to system identification when the difference arises between the right and left eigenvectors corresponding to the same eigenvalue. The identification of non-self-adjoint system is of great importance for the prediction of flutter boundary, the identification of control law, the optimal design of structures etc. However, for the non-self-adjoint system in engineering (e.g. bridge flutter, the aerodynamic drag forces acting on airplane wings and fuselages, the forces acting on the rotor in turbines, brake system of a vehicle), the identification is based on the output data of the system because of the unknown input data. This research concerns the operational modal analysis (OMA) of a typical non-self-adjoint system. Specifically, the equivalence between the correlation functions of random responses and the free decay responses of the original structure is proved for the non-self-adjoint system. The ERA method is applied to reconstruct the non-self-adjoint system. Case examples on the identification of a six-degree-of-freedom system and the flutter derivatives of bridge sections are performed to validate the method. © 2018, Nanjing Univ. of Aeronautics an Astronautics. All right reserved.