According to DNA studies, the iconic trees first arose in Madagascar 21 million years ago.
Their seeds were later carried on ocean currents to Australia and also to mainland Africa, evolving into distinct species.
The researchers are calling for greater conservation efforts for the trees, which they say may be closer to extinction than previously thought.
Baobabs are known as “the tree of life” or “upside down tree” for their strange shapes and longevity. They are in trouble because of a combination of drought and rising temperatures.
Dr Ilia Leitch, of the Royal Botanic Gardens, Kew, worked on the study, alongside her husband, Prof Andrew Leitch, of Queen Mary University of London.
“We have been able to pinpoint the origin of baobabs, which are an iconic keystone species supporting a wide diversity of animals and plants as well as humans,” she told the BBC.
“And the data have enabled us to provide important new insights which will inform their conservation to safeguard their future.”
The researchers studied eight baobab species, six of which are found in Madagascar, one widespread across Africa, and another in north-west Australia.
They are calling for a higher conservation status for two endangered Malagasy species, including the biggest and most famous of Madagascar’s baobabs, the giant baobab.
The trees can live for thousands of years, growing to a huge size and storing large amounts of water in their trunks to survive through the dry seasons.