Plants are the basis of all human life; they provide food and feed, medicine and drugs, and raw materials for clothing, housing and energy production. Due to global change, the role of crop plants as the foundation of human civilisation becomes threatened. Therefore, innovative strategies for crop improvement are required that aim at enhancing crop productivity while minimizing resource requirements. In this context, the CEPLAS mission is to contribute new paradigms to solve urgent problems in plant performance and production through exploitation of natural variation and biodiversity. CEPLAS holds a unique position within the German Excellence Initiative as the only cluster focusing exclusively on plant science. It applies a new approach that is driven by evolutionary analysis and synthetic biology. CEPLAS aims to understand the genetic architecture and the regulatory networks of four important complex traits at the level of a quantitative model followed by the synthesis of the trait’s modules and sub-modules. Based on this combination of evolutionary analysis and synthetic biology paradigmatic solutions shall be provided for: [A] Annual and perennial life histories, [B] C4 photosynthesis, [C] Plant-microbe interactions and [D] Metabolic interaction. Connecting evolutionary and synthetic biology will not only aid in understanding the architecture and the mechanistic functioning of complex traits, but the design and synthetic phase will also feed back to understanding the evolutionary process.