In the post-genomic era, it is important to analyze interaction networks that include genes, proteins, enzymes and compounds such as a metabolic pathway. Every organism has such networks individually. However, several parts of them are conserved in different organisms. The purpose of this analysis is to extract sub-networks composed of these common elements through the phylogenetic analysis. We extracted network modules from metabolic pathways using phylogenetic profile and cluster analysis. The enzymes of these modules are related by evolutionary and functional correlation. Our results give a valuable insight into the evolution of metabolic pathways.