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This correspondence presents the application of an existing deadlock-free resource allocation control method for a reconfigurable manufacturing system (RMS) with serial and parallel configuration, and further proposes a new higher level deadlock avoidance control method. RMSs have been introduced to replace traditional large-volume production systems such as dedicated manufacturing systems, adding more flexibility and convertibility. Such manufacturing systems require that their controls be changed rapidly to cope with unpredictable market demands; their desired control behaviors must also be verified in advance of running the system to reduce the ramp-up time. One important desired control behavior is the deadlock freeness in the resource allocation. A rule-based matrix method that has been proposed to develop deadlock-free resource allocation control is applied to an example RMS with serial and parallel configuration. Through this application, higher level deadlocks were found in the example RMS that are not prevented with the existing method. A new control method to avoid the higher level deadlocks is developed.