This paper presents the state of archaeobotanical research at rock shelters and cave sites in Island Southeast Asia and its potential for enhancing our knowledge of the region's prehistory. It takes stock of what has been done, what is being done, and the prospects for archaeobtanical research in the region. This paper argues that the knowledge we generate from archaeobotany, in tandem with other methodologies, can lead to a better understanding of past subsistence strategies in the region. It also takes the view that knowledge derived from analyzing cave deposits is better utilized when seen in relation to the wider human landscape, at whatever scale a study takes.