Frequent changes regarding products, processes, and technologies require the manufacturing systems and the control systems to be inexpensive, flexible, and easy to re-configure. The major aim of the research presented in this paper is to define a generic reference architecture that supports design and implementation of highly flexible control-systems for manufacturing cells. Based on the analyses of two machining cells, a preliminary version of such an architecture has been developed. The main features of this are: (1) modular control structure with one module for each resource in the cell, (2) message-based, generic communication between the system's modules, (3) separation of generic and specific control activities, and (4) separation of the products' operation lists from the description of the resources' capabilities. Among manufacturing cells in the industry, there is a great variety considering system layout, product flow, and the resources' capacity, flexibility, and operation. Therefore, in order to gain a more generic architecture for manufacturing systems, different types of production resources available, processes, manufacturing system layouts, and product flows have been analysed and classified based on information gathered in an industrial survey. Based on this analysis, the applicability of the architecture is discussed. It is concluded that the architecture is directly applicable to most cells, and if some modifications are made in the architecture in order to handle specific features observed, the architecture could be made applicable to all cell types defined except one.