This paper presents the identification of the aerodynamic model of the "Flying-V", a novel aircraft configuration. The aerodynamic model is estimated using flight test data from a 4.6% sub-scale model. The dataset includes longitudinal and lateral-directional maneuvers performed by both the pilot and the autopilot to excite the aircraft dynamic modes. The so-called Two-Step Method is used to decouple and simplify the aerodynamic identification problem; the state estimation step is performed by an Iterated Extended Kalman Filter, and the parameter-estimation step using ordinary least squares. A stepwise regression technique and previous knowledge from wind-tunnel tests are combined to select the model structure, and the identified model is validated using a third of the gathered data. The estimated models are parsimonious and considered adequate in terms of model fit, with a maximum relative Root Mean Square Error of 10% for the worst validation case. For the considered location of the center of gravity and flight conditions, the estimated aerodynamic derivatives confirm that the aircraft is longitudinally stable, both statically and dynamically; and that it is also laterally and directionally statically stable. The analysis of the dynamic modes of the sub-scale model showed stable short period and roll subsidence modes, a lightly damped Dutch roll mode, and lightly damped/unstable phugoid and spiral modes.