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In this paper, an efficient algorithm for finding optimal deadlock-free schedules in a Flexible Manufacturing System (FMS) modeled by a kind of Petri net, Systems of Simple Sequential Processes with Shared Resources (S4R) nets, is presented. This algorithm is based on an effective Genetic Algorithm (GA) search method, and the structural elements analysis of the Petri net. In order to find the optimum and deadlock-free scheduling strategy from the population generated by the GA, a Petri net structural analysis procedure is involved as a criterion to select among the populations and to make the job scheduling deadlock-free. The effectiveness and efficiency of the proposed approach is illustrated using an example.