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This paper presents a decentralized approach for the local reconfiguration of control software, which is based on a multiagent system with ontology-driven reasoning. We apply this approach to a transportation system and demonstrate improvements on efficiency, fault tolerance and stability with several experiments. One key element to achieve these results is the use of ontologies to ensure the consistency of local reconfiguration of the control software with the desired global behavior of the system. To show the feasibility of our approach in a realistic industrial setting, we implemented the multiagent system on the “Testbed for Distributed Holonic Control” at the Automation and Control Institute. We also used simulation to analyze its impact on the system performance. The simulation results as well as the real system experiments indicate that our approach is able to cope with the dynamic nature of the transportation domain thereby enhancing reconfigurability, robustness, and fault tolerance.