Molecular discreteness would be important in intracellular chemical reactions since the number of copies of molecules included in the reactions is small compared to in vitro situations [1][2][3][4][5]. Recently an experimental evidence for the significance of the molecular discreteness was found [6]. For a theoretical study, Togashi and Kaneko [3] reported a new transition phenomenon in a small autocatalytic system by a discrete stochastic simulation of the system. It cannot be observed in a model based on the classical reaction rate equation. However, Ohkubo et al. [7] found that the transition phenomenon reported However, we use CLE as a reference model in order to investigate the discrete nature of chemically reacting systems J. Comput. Chem. Jpn., Vol. 9, No. 3, pp.135-142 (2010) © The aim of this paper is to investigate the discrete nature of chemically reacting systems. In order to achieve our purpose we propose a systematic method to compare the discrete stochastic model of chemically reacting systems with the continuous stochastic model. We adopt the chemical master equation ( well-known idea of approximating diffusion processes by birth-death processes, we construct a family of master equations parameterized by the degree of discreteness. This family of master equations bridges CME and CFPE.With full degree of discreteness we obtain CME and as decreasing discreteness the family of master equations converges to CFPE. Our strategy is not to study CME directly but to distinguish the properties of CME by putting CME into the family of master equations bridging CME and CFPE. We examine the usefulness of our construction by two simple examples.