Though the designers of Flexible Manufacturing Systems (FMS) strive to ensure the maximum flexibility in the system, in practice, after the implementation of such systems the operational executives often find it hard to accommodate frequent variations in the part designs of incoming jobs. This difficulty can very well be overcome by scheduling the variety of incoming parts into the system efficiently. In this work an appropriate scheduling mechanism is designed to generate a nearer-to-optimum schedule using Genetic Algorithm (GA) with two different GA Coding Schemes. Two contradictory objectives of the system were achieved simultaneously by the scheduling mechanism. The results are compared with those obtained by different scheduling rules and conclusions are presented.