The rise of the Panama Isthmus was the last step in the closure of the circumtropical seaways. The closure of the Panama Isthmus had fundamental consequences for global ocean circulation, evolution of the tropical ecosystems and potentially influenced the switch to the modern cold house climate mode. The Atlantic and Pacific marine ecosystems became gradually separated whereas terrestrial organisms suddenly had the means to migrate between North and South America. Combining high-resolution geochemical proxies for the closure history with data on fossil distributions and genetic data provides independent evidence on the closure history. These datasets provide new boundary conditions for Earth System models to simulate the effects of palaeoceanographic change on global climate and allow exploration of hypotheses for the Northern Hemisphere glaciation.