In this paper, a novel approach for designing chromosome has been proposed to improve the effectiveness, which called multistage operation-based genetic algorithm (moGA). The objective is to find the optimal resource selection for assignments, operations sequences, and allocation of variable transfer batches, in order to minimize the total makespan, considering the setup time, transportation time, and operations processing time. The plans and schedules are designed considering flexible flows, resources status, capacities of plants, precedence constraints, and workload balance in Flexible Manufacturing System (FMS). The experimental results of various Advanced Planning and Scheduling (APS) problems have offered to demonstrate the efficiency of moGA by comparing with the previous methods. Categories and Subject Descriptors F.2.1 [Numerical Algorithms and Problems] General Terms Algorithms. Keywords Resource Selection and Operation Sequences, Multistage Operation-based Genetic Algorithm ...