question: Genome-wide physical protein-protein interaction (PPI) mapping remains a major challenge for current technologies. Here, we report a high-efficiency yeast bimolecular fluorescence complementation method coupled with next-generation DNA sequencing (BiFC-seq) for interactome mapping. We applied this technology to systematically investigate an intraviral network of Ebola virus (EBOV). Two-thirds (9/13) of known interactions of EBOV were recaptured and five novel interactions were discovered. Next, we used BiFC-seq method to map the interactome of the tumor protein p53. We identified 97 interactors of p53 with more than three quarters are novel. Furthermore, in more complex background, we screened potential interactors by pooling two BiFC-libraries together, and revealing a network of 229 interactions among 205 proteins. These results show that BiFC-seq is a highly sensitive, rapid and economical method in genome-wide interactome mapping.