Recently, advances in high-throughput experimental technologies enable an ever-increasing amount of data on protein interaction networks available. These data provide new insights into the evolutionary processes of protein interaction networks. The researches associated with analyzing such data from an evolutionary perspective was reviewed at five different levels: from proteins to protein interactions, motifs, modules and the whole network. Two aspects were focused on: 1) the constraints of the network organization on protein evolution, 2) origins and evolution of the topological features of protein interaction networks which are different from those of random networks. In addition, the enlightenments from the former studies were presented and the development trends in this field were discussed.