The system identification problem of Multi-Input Multi-Output fractional order systems with Time-Delay is studied. A Frequency-Domain identification algorithm is presented, which combines genetic algorithm and subspace method for fractional order systems with time-delay in state. The genetic algorithm is used to identify fractional differential order and Time-Delay parameter. And the state space model is obtained by using frequency-domain subspace method when fractional differential order and time-delay parameter are fixed. Numerical simulation results validate the proposed algorithm.