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This paper studies the synchronization of fractional-order chaotic systems in the presence of unknown external disturbances. A new disturbance identification method using fractional-order algebraic identification is proposed to handle unknown disturbances. In order to guarantee system stability, the nonlinear state-feedback controller is designed based on the Lyapunov theory. All system parameters and orders, as well as the external disturbances, are considered time-varying in this paper. The simulation results show that the estimation of unknown disturbance is executed more quickly and accurately using the proposed method, which also leads to fast and precise synchronization of the chaotic systems. A circuit implementation is also performed to identify the unknown disturbances in a fractional-order electronic chaotic oscillator system to evaluate the practicability of the proposed approach.