Rainforests are often described as the world's last virgin landscapes; however hunter-gatherers may have been modifying these environments for over 50,000 years. Despite this, the antiquity of early tropical forest exploitation by hunter-gathers and the transition to farming are still poorly understood. Today globalization drives deforestation of rainforests at an unprecedented rate. The forest, the lives of its present-day inhabitants, and the archaeological evidence for their history are unlikely to survive for much longer in their present form. The 'Cultured Rainforest Project', an interdisciplinary project involving anthropologists, archaeologists and palaeoecologists, was set up in 2007 to investigate the long-term and present-day interactions between people and the rainforest in the Kelabit Highlands of central Borneo, so as to better understand past and present agricultural and hunter-gatherer lifestyles and landscapes. This paper examines the environmental evidence used to investigate initial signs of plant exploitation and the transition to agriculture, as well as to understand the wider significance of past plants in a changing cultural landscape. Results have shown that two pronounced cultural waves of human-plant interactions took place in the Kelabit Highlands during the late Holocene; although tentative marks may be present on the landscape ca.7000-6000 years ago. The first pronounced wave of human-plant interaction begins from at least 3000 cal. BP. It seems to correspond with the appearance of stone mounds and open-air sites recorded in the archaeological record. The sago palm Eugeissona plays an important role during this period. A second wave of cultural activity, particularly in the last 450 years, is recorded in the southern Kelabit Highlands and is marked by rice becoming important. This may be linked to the construction of a wide range of different megaliths and earthworks, due to its inferred association with wealth and status in prehistoric and historic periods. It is perhaps also linked to a rise in trade between the coastal regions and highlands.