In this paper, the procedure of system identification by prediction error method, using nonlinear restoring force model, is presented, and several system identifications of two base-isolated structures using two-directional recorded seismic response are carried out. In the system identifications, the restoring force of the base isolation system is assumed to consist of several piecewise restoring force models, including multiple shear spring model. As results of using trilinear multiple shear spring models, both the estimated hysteresis shapes and the time histories show good agreement with those obtained directly from the observed data.