This paper proposes a control scheme for a wave energy conversion system based on a linear generator and a cascaded multilevel converter. The mechanical conversion system is composed of a buoy connected directly to a linear generator. The windings of the generator are individually controlled by a cascaded multilevel power converter using independent maximum power point tracking to improve energy harvesting. The output of the cascaded converter is controlled to keep the DC capacitors balanced and generate a multilevel voltage at the output terminals which reduces the losses in the underwater transmission line. Experimental results show the performance of the proposed control scheme maximizing the power generation by imposing a current with the same waveform of the induced voltage and balancing the DC capacitors.