Indonesia–Madagascar relations spans for over a millennium, since the ancestors of the people of Madagascar sailed across the Indian Ocean from the Nusantara Archipelago back in 8th or 9th century AD.

According to an extensive new mitochondrial DNA study, native Malagasy people today can likely trace their genetic heritage back to 30 different mothers from Indonesia.

[3] Malagasy contains loan words from Sanskrit, all with local linguistic modifications via Javanese or Malay, hint that Madagascar may have been colonized by settlers from the Srivijaya empire.

[8]: 114–115 Javanese trading and slaving activities in Africa caused a strong influence on boat-building on Madagascar and the East African coast.

But it is certain that they formerly navigated to the Cape of Good Hope and were in communication with the east coast of the island of São Lourenço (San Laurenzo — Madagascar), where there are many brown and Javanese-like natives who say they are descended from them.

The treacherous Cinnamon shipping route took vessels from Indonesian waters across the Indian Ocean past the Seychelles, Madagascar, and South Africa to Ghana.