The Arabidopsis Interactome Mapping Consortium has developed a high-quality binary protein-protein interaction map for *Arabidopsis thaliana*, containing approximately 6,200 reliable interactions between 2,700 proteins. This map, named *Arabidopsis* Interactome version 1 (AI-1MAIN), was generated using an improved high-throughput binary interactome mapping pipeline based on the yeast two-hybrid system. The quality of AI-1MAIN was validated against a positive reference set and a random reference set, with a precision of about 80%. The map reveals a global organization of plant biological processes and identifies numerous novel hypothetical functional links between proteins and pathways. The study also highlights dynamic rewiring of interactions following gene duplication events, providing evidence for evolution acting upon interactome networks. This work should facilitate systems approaches to better understand plant biology and improve crop development.The Arabidopsis Interactome Mapping Consortium has developed a high-quality binary protein-protein interaction map for *Arabidopsis thaliana*, containing approximately 6,200 reliable interactions between 2,700 proteins. This map, named *Arabidopsis* Interactome version 1 (AI-1MAIN), was generated using an improved high-throughput binary interactome mapping pipeline based on the yeast two-hybrid system. The quality of AI-1MAIN was validated against a positive reference set and a random reference set, with a precision of about 80%. The map reveals a global organization of plant biological processes and identifies numerous novel hypothetical functional links between proteins and pathways. The study also highlights dynamic rewiring of interactions following gene duplication events, providing evidence for evolution acting upon interactome networks. This work should facilitate systems approaches to better understand plant biology and improve crop development.