Spread Spectrum applications require a set of sequences with individually peaky auto-correlation and pair-wise cross-correlation. Obtaining such sequences is a combinatorial problem. If the auto-correlation and cross-correlation are taken in the aperiodic sense then there are hardly any theoretical aids available. Thus the problem of signal design referred to above is a challenging problem for which many global optimization algorithms like Genetic Algorithm, Simulated Annealing and Tunneling Algorithm were reported in the literature. Recently an efficient VLSI architecture for Generation of the Six phase codes was proposed. Integrating this generation architecture with the currently proposed identification architecture provides an efficient Real-Time Hardware solution for identification and generation of the Six phase codes. The paper aims at an efficient hardware implementation of the Modified Genetic Algorithm (MGA) for the synthesis of optimal Six-Phase codes useful for Spread Spectrum applications. The VLSI System is implemented on the Field Programmable Gate Array (FPGA) as it provides the flexibility of Reconfigurability and Reprogramability.