Interrogating protein complexes and pathways in an evolutionary context provides insights into the formation of the basic functional components of the cell. We developed two independent Cytoscape plugins that can be cooperatively used to map evolving protein interaction networks at the module level. The APCluster plugin implements a recent affinity propagation (AP) algorithm for graph clustering and can be applied to decompose networks into coherent modules. The NetworkEvolution plugin provides the capability to visualize selected modules in consecutive evolutionary stages.