In the areas adjacent to the drowned Pleistocene continent of Sunda – present-day Mainland and Island SE Asia – the Austronesian Hypothesis of a diaspora of rice cultivators from Taiwan ∼4200 years ago has often been linked with the start of farming. Mounting evidence suggests that these developments should not be conflated and that alternative explanations should be considered, including indigenous inception of complex patterns of plant food production and early exchange of plants, animals, technology and genes. We review evidence for widespread forest disturbance in the Early Holocene which may accompany the beginnings of complex food-production. Although often insubstantial, evidence for incipient and developing management of rainforest vegetation and of developing complex relationships with plants is present, and early enough to suggest that during the Early to mid-Holocene this vast region was marked by different approaches to plant food production. The trajectory of the increasingly complex relationships between people and their food organisms was strongly locally contingent and in many cases did not result in the development of agricultural systems that were recognisable as such at the time of early European encounters. Diverse resource management economies in the Sunda and neighbouring regions appear to have accompanied rather than replaced a reliance on hunting and gathering. This, together with evidence for Early Holocene interaction between these neighbours, gives cause for us to question some authors continued adherence to a singular narrative of the Austronesian Hypothesis and the ‘Neolithisation’ of this part of the world. It also leads us to suggest that the forests of this vast region are, to an extent, a cultural artefact.