This paper presents the system identification and control of an unmanned helicopter(UH) with ducted fan. The plant is an unstable multi-input-multi-output (MIMO) system. First, four identification methods have been considered in this work. Two of these methods studied the identification of the system as a set of transfer functions relating different inputs and outputs, namely the least square method with QR-factorization (LS-QR) and the recursive least square method (RLS). The other two methods are state-space identification method. Indeed, the classical subspace identification method and the observer-Kalman filter identification (OKID) method have been used to identify the system in state space representation. Analytical formulations of these methods as well as comparison of their performances based on their degree of fitness are presented for the special case of UH system. The results show that OKID out-performs the other methods. Based on this result, an OKID-LQGI-based controller for velocities tracking controller is proposed. The simulation results show excellent tracking performance.