A novel intelligent genetic algorithm (GA), called Minimum Distance guided GA (MDGA) is proposed for peak-average-power ratio (PAPR) reduction based on partial transmit sequence (PTS) scheme in a synchronous Multi-Carrier Code Division Multiple Access (MC-CDMA) system. In contrast to traditional GA, our MDGA starts with a balanced ratio of exploration and exploitation which is maintained throughout the process. It introduces a novel replacement strategy which increases significantly the convergence rate and reduce dramatically computational complexity as compared to the conventional GA. The simulation results demonstrate that, if compared to the PAPR reduction schemes using exhaustive search and traditional GA, our scheme achieves 99.52% and 50+% reduction in computational complexity respectively.