Biodiversity is the basis for agriculture and for a sustainable future. More than 1.9 million living species have been described; millions more have gone extinct, including major branches of the tree of life. The distribution of this biological diversity is variable in space and time, although it is becoming more homogeneous as a result of globalisation. Only a few hundred species of plants and animals have been domesticated over the past 10 000 years, yet they are essential for the livelihoods of people worldwide. New tools are giving us insights into the origins of agriculture, as well as opening new possibilities for using and changing the genetic diversity of these crops and races. This can have a major impact on the wellbeing of present and future generations. Agriculture is also having major impacts on natural ecosystems. An estimated 25% of terrestrial ecosystems have been transformed into production systems, mostly in the past 50 years. Habitat loss and fragmentation, pollution and invasions are some of the impacts. Climate change is likely to have additional impacts that will alter the distribution and abundance of biodiversity, as well as the interactions among species. It is time to bring together knowledge from biodiversity science and agriculture through a whole-system approach. A better understanding of the diversity, distribution, evolution and ecology of life is essential for a sustainable future. It can also open new avenues for agriculture and food security.