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This paper presents a design of a dispatching control system for flexible manufacturing systems with dynamic order arrival. The design is a multi-agent implementation of the holonic manufacturing system architecture PROSA. The dispatching control system combines two main subsystems: a routing dispatcher and a resource dispatcher. The routing dispatcher offers routing flexibility by utilising the subnet capability concept together with ant-based route exploration, while the resource dispatcher brings the operation flexibility offered by the resources. Combination of the routing dispatcher and the resource dispatcher offers more flexibility to control the internal logistics of manufacturing systems. Furthermore, the control is designed to accommodate the earliness/tardiness cost optimisation objective.