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Flexible flow shop (FFS) has multiple machines in each stage, and usually not all the machines of a stage, but a subset of them can be assigned to a job because of various constraints. Recent studies have considered the inner-stage constraints, and this paper addresses the inter-stage constraints between two successive working centers. Traditional genetic algorithm (GA) is not applicable because its chromosome becomes too long when the problem size increases. This paper proposes serial-number coding scheme (SCS) firstly, which can shorten chromosome length substantially. Then switching SCS (SSCS) is developed further to reduce hamming distance between neighboring solutions. SSCS based genetic algorithm (SSGA) shows better computability and performance than traditional genetic algorithm.