In this paper, a job shop scheduling system is developed which can cope with the changes of shop floor status with flexibility. This system suggests near optimal sequence of operations by using Genetic Algorithm which considers alternative process plans. The Genetic Algorithm proposed in this paper has some characteristics. The mutation rate is differentiated in order to enhance the chance to escape a local optimum and to assure the global optimum. And it employs the double gene structure to easily make the modeling of the shop floor. Finally, the quality of its solution and the computational time are examined in comparison with the method of a Simulated Annealing.