In 2001, the Earth System Science Partnership declared an urgent need to develop 'strategies for Earth System management'. Yet what such strategies might be, how they could be developed and how effective, efficient and equitable such strategies would be, remain unspecified. We argue that the institutions, organizations and mechanisms by which humans currently govern their relationship with the natural environment and global biogeophysical systems are both insufficient and poorly understood. For this reason, we have developed, and present here, the science and implementation plan for the Earth System Governance Project, a new 10-year global research agenda under the auspices of the International Human Dimensions Programme on Global Environmental Change (IHDP) and the Earth System Science Partnership (ESSP).