This chapter introduces evolutionary analyses of protein interaction networks and of proteins as components of the networks. The authors show relationships between proteins in the networks and their evolutionary rates. For understanding protein-protein interaction (PPI) divergence, duplicated genes are often compared because they are derived from a common ancestral gene. In order to reveal evolutionary mechanisms acting on the interactome it is necessary to compare PPIs across species. Investigation of co-localization of interacting genes in a genome shows that PPIs have an important role in the maintenance of a physical link between neighboring genes. The purpose of this chapter is to introduce methodologies for analyzing PPI data and to describe molecular evolution and comparative genomics insights gained from such studies.