Existing modeling frameworks for manufacturing system control can be classified into hierarchical, heterarchical, and hybrid control frameworks. The main drawbacks of existing frameworks are discussed in this paper. A new hybrid modeling framework is also described. It is a hybrid of the two: hierarchical and heterarchical frameworks. In this proposed framework, entities (e.g., parts) and resources (e.g., material handling devices, machines, cells, departments) are modeled as holonic structures that use intelligent agents to function in a cooperative manner so as to accomplish individual, as well as cell-wide and system-wide objectives. To overcome the structural rigidity and lack of flexibility, negotiation mechanisms for real-time task allocation are used. Lower-level holons may autonomously make their negotiations within the boundary conditions that the higher-level holons set. Horizontal, as well as vertical decisions, are made between various levels of controllers, and these are explicitly captured in the model.