Marine current turbine (MCT) have been widely used nowadays, it is important to monitor their health state. Unnecessary marine biological growth or marine pollutants attached to the moving parts will affect the operation of the system by introducing imbalance. The imbalance, regarded as faults, would change the performance of turbine and lead to progressively increasing damages. In this paper, a marine current turbine prototype with permanent magnet synchronous generator (PMSG) has been studied. An innovative imbalance fault detection method is proposed for marine current turbines under the condition of wave and turbulence. In the proposed method, the average frequency of current is calculated through synchronous sampling. Meanwhile, current fluctuation influence is reduced during one revolution. The empirical mode decomposition (EMD) and spectrum analysis are used to achieve fault characteristics. Theoretical analysis, simulation and experimental results under different conditions validate the proposed method. Moreover the proposed method could be used for long-term marine current turbine monitoring in respect to its simplicity and low time cost.