A system identification procedure is developed to identify the physical parameters of structures with seismic isolation using the friction pendulum systems (FPSs). The superstructure is assumed to be linear on account of substantial reduction of seismic forces with the installation of FPS. Hysteretic models of both Coulomb's and Mokha's friction mechanism have been considered for the FPS. Simulation results indicate that the physical parameters of the FPS and superstructure can be successfully identified by the proposed scheme. Experimental verification has been conducted further via shaking table tests using realistic earthquake scenarios. The identified parameters from seismic response data indicate that the FPSs behave in better agreement with Mokha's friction mechanism than Coulomb's. Feasibility of the proposed scheme in the identification of FPS-isolated structures using seismic data has been verified. This may facilitate in-situ performance assessment of structures isolated with sliding-type isolation systems.