Robust identification of lightly damped flexible structures, because of high amplitude modes in resonance frequencies, is a challenging task. In this paper, two different methods for robust identification of a lightly damped flexible beam arc applied and compared. The first method is called NSSE using stochastic assumptions on the uncertainties and the second one is ellipsoid set-membership method by deterministic assumptions on the noise and unmodelled dynamics. Identification results show that NSSE with integrated random walk process gives better model for the in-bandwidth modes and unmodelled dynamics in comparison with other specified methods. In fact the identified model will exhibit a good compromise between the performance and robust stability of the controller designed base on it and its uncertainty band.