Tree crops are a very important part of the agricultural systems of the Pacific and elsewhere in the tropics, but are poorly accommodated in the usual frameworks within which the status, origins and development of food production are discussed. These frameworks reflect classifications in which deeply embedded and problematic assumptions about nature, culture and production are represented in confused terminological distinctions, forcing subtle and complex local practices into overly simplistic dichotomies. Key concepts, notably domestication, further constrain ideas about past and present subsistence. Rethinking these conceptual frameworks with examples drawn from tree crops, this paper suggests more productive approaches to the complexities of tropical forest-based agricultural systems. These approaches include a shift of analytical frame from the characteristics of individual crops to agrodiversity and the linkages among different categories of crops and different kinds of management; a reconsideration of domestication and how human selection operates on tree and tree-like crops; and a discussion of the significance of the genetic diversity of landraces characteristic of traditional agricultural systems. This critique aims to clarify understanding of the origins and development of agroecosystems by considering a broader range of crop types and practices than is usual, and by emphasizing the importance of multidisciplinary, multifocal research.