In-flight identification of an aircraft's dynamic model can benefit adaptive control schemes by providing estimates of aerodynamic stability derivatives in real time. This information is useful when the dynamic model changes severely in flight such as when faults and failures occur. Moreover a continuously updating model of the aircraft dynamics can be used to monitor the performance of onboard controllers. Flight test data was collected using a sum of sines input implemented in closed loop on a twin engine, fixed wing, Unmanned Aerial Vehicle. This data has been used to estimate a complete six degree of freedom aircraft linear model using the recursive Fourier Transform Regression method in frequency domain. The methods presented in this paper have been successfully validated using computer simulation and real flight data. This paper shows the feasibility of using the frequency domain Fourier Transform Regression method for real time parameter identification.