The centre of origin of coconut extends from Southwest Asia to Melanesia. Nevertheless, its pre-Columbian existence on the Pacific coast of America is attested. This raises questions about how, when and from where coconut reached America. Our molecular marker study relates the pre-Columbian coconuts to coconuts from the Philippines rather than to those of any other Pacific region, especially Polynesia. Such an origin rules out the possibility of natural dissemination by the sea currents. Our findings corroborate the interpretation of a complex of artefacts found in the Bahía de Caraquez (Ecuador) as related to South-East Asian cultures. Coconut thus appears to have been brought by Austronesian seafarers from the Philippines to Ecuador about 2,250 years BP. We discuss the implications of molecular evidence for assessing the possible contribution of early trans-pacific travels to and from America to the dissemination of domesticated plants and animals.