Comparative analyses of the metabolic networks among different species provide important information regarding the evolution of organisms as well as pharmacological targets. In this paper, a method is proposed for comparing metabolic networks based on enzymatic reactions within different species. Specifically, metabolic networks are handled as sets of enzymatic reactions. Based on the presence or absence of metabolic reactions, the metabolic network of an organism is represented by a bit string comprised of the digits “1” and “0, ” called the “reaction profile.” Then, the degree of similarity between bit strings is defined, followed by clustering of metabolic networks by different species. By applying our method to the metabolic networks of 33 representative organisms selected from bacteria, archaea, and eukaryotes in the MetaCyc database, a phylogenetic tree was reconstructed that represents the similarity of metabolic network based on metabolic phenotypes.