The accumulation of recent data from archaeobotany, archaeozoology and Neolithic excavations from across South Asia warrants a new overview of early agriculture in the subcontinent. This paper attempts a synthesis of these data while recommending further systematic work and methodological developments. The evidence for origins and dispersals of important crops and livestock from Southwest Asia into South Asia is reviewed. In addition evidence for indigenous plant and animal domestication in India is presented. Evidence for probable indigenous agricultural developments in Gujarat, the Middle Ganges, Eastern India, and Southern India are reviewed. An attempt is made to highlight regions of important frontiers of interaction between early farmers and hunter-gatherers. The current evidence suggests that the Neolithic trajectories in different parts of South Asia differ from each other. Indigenous centers of plant domestication in India also differ from the often discussed trajectory of Southwest Asia, while suggesting some similarities with agricultural origins in Africa and Eastern North America as well as secondary agricultural developments on the peripheries of Eurasia.