A frequency domain subspace identification of fractional order systems with input time-delay is studied in this paper. A new identification method, which combines the merits of differential evolution (DE) algorithm and subspace identification algorithm in frequency domain, is presented. For the optimal search of fractional commensurate differential order and time delay parameters, the DE algorithm is applied. For fixed fractional commensurate differential order and time delay, subspace method is performed to obtain the state space model. Simulation results validate the proposed fractional order system identification method.