PNmerger (a biological Pathway and protein Network merger) is a java based plugin for the widely used open source Cytoscape molecular interaction viewer. For a protein interaction network, PNmerger can automatically annotate the network proteins with the KEGG pathway information, find the known pathway elements in protein network, and predict the possible pathway elements. To present the pathway information for the protein network, PNmerger illustrates the clusters of the nodes with the same biological pathway, and also presents the potential crosstalk elements between different pathways. This information will be helpful for the users to find the important clues for knowledge discovery and experimental design. PNmerger is available online at http://www.hupo.org.cn/PNmerger.