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Deadlock must be avoided in a manufacturing system. In this paper, an efficient algorithm for finding a good deadlock-free schedule in a manufacturing system with enough (sufficient) or limited buffer is presented. This algorithm is based on the effective genetic algorithm (GA) search method. A formal Petri net structure is introduced, and the token player is used to assure deadlock freeness. In order to make the scheduling strategy generated by GA meet the required deadlock-free constraint, a Petri net is involved in checking the implementation of a manufacturing system during the job-scheduling process. The effectiveness and efficiency of the proposed approach is illustrated by several examples.