Due to the need for clean and efficient automobile propulsion systems, this paper models an important process in the enabling of homogeneous charge compression ignition (HCCI) engines. The need for a deep understanding of charge-residual mixing in residual-affected HCCI engines requires a model of the chemical composition during the mixing process. In this paper, a chemical composition model is developed specifically for a two-zone mixing model to account for important phenomena such as the presence of unburned fuel in the residual exhaust gas. The model is developed as a control-oriented model that can be used for real-time decision making and control. This paper develops the composition model for the major species present, and also presents the method that would be used to include other minor species. The model is simulated for variations in residual gas fraction equivalence ratio, a misfire situation, and its effects on air/fuel ratio.