This paper describes system identification of a light weight, high aspect-ratio flying-wing type aircraft. For this aircraft, complex flexible structure poses challenges in correctly iden- tifying and validating the aircraft structural modes. Also, structural deformation coupled with unsteady aerodynamics in flight makes aerodynamic characterization difficult. The aircraft is identified in flight with inputs carefully selected to excite the dynamic modes of interest. In this study, the lightly damped structural modes are identified based on spectral analysis. The aerodynamic parameters are estimated using prediction error methods. The results of the estimation are validated on data at different flight conditions, as well as by comparison to subspace based black box models. A focus of the paper lies on providing useful insights and lessons learned during the flight test campaign.