A large amount of genomic information is currently being generated in the biological sciences; however, the postgenome era needs biological connectors to bridge between genome data and gene functions. Interactomes are protein-protein interaction maps used to study gene function through the demonstration of predicted functions based on known roles of interaction partners to understand biological processes as a systemic approach. Diverse experimental approaches for interactomes have been developed, each of which has its own merits and pitfalls. In this review, the status and application of the yeast two-hybrid (Y2H)-based plant interactome is introduced to investigate gene functions as a biological network.