Permanent magnet synchronous generators (PMSG) based marine current system has gained much attention due to several advantages such as high predictability, rapid response and high-power density. The performance and power integration efficiency of the above-mentioned system greatly rely on the applied control system. However, system nonlinearities, parameter variations make the controller design process a challenging task. This paper introduces passivity based fuzzy fractional order proportional integral and derivative (PID) controller for PMSG based marine current energy conversion system under swell effect and parameter uncertainties. The proposed approach combines a new passivity-based current control (PBCC) with a fuzzy fractional order PID control (FFO-PID). The proposed method is tested under the swell effect and parameter uncertainties using MATLAB/Simulink. The proposed controller exhibits robustness against swell effect, parameter changes and shows fast convergence of the system states. Furthermore, the exponential stability and error convergence of the proposed controller is analytically justified.