In this paper, using both linear and nonlinear identification methods based on iterative and recursive least-square, the performance of a backstepping control system of a quadrotor in the presence of uncertainties is improved. At first, the dynamic model of a quadrotor is introduced and descriptive equations are presented in an appropriate state-space in order to design a controller based on backstepping method. Then the backstepping controller is designed using virtual controller for trajectory tracking. In this control system, the control performance is not satisfying because of the physical uncertainties existed in quadrotor. Consequently, an online identification method is introduced and used to improve the performance of the controller. In this regard, some parameters, which are linear in the model structure, are identified by least square error technique and iterative least square method is used for identifying other parameters.The results indicate that the steady-state error is decreased and the ability of tracking of a desired trajectory in the presence of uncertainties is increased. Furthermore, the result demonstrate the stabilization of roll and pitch angles, while, the method prevents the vibration of control forces.