This paper offers a critical examination of the use of the concept of ontology in ethnobotany. Competing definitions and problems are first assessed for recent work in anthropology and the history of science. This is followed by a review of seven areas of current ethnobotanical investigation where there are disjunctions of approach that could arguably be said to be ontological: post-Linnean taxonomic orthodoxy versus local plant classification, pre-Linnean natural history versus science, phytopharmaceutical orthodoxy versus medical anthropology, museum practice versus lived practice, ecological versus phylogenetic explanation, plant versus knowledge movement, and shifts in understanding contingent on membership of different intra-cultural domains. In the light of these examples, a threefold meta-conceptual distinction is suggested: between cultural domains (distinguishing knowledge and practice on the grounds of content), epistemes (distinguishing knowledge in terms of the methods and approaches used to acquire it), and ontologies in the strict sense (defined in terms of underlying logical relations and cosmological assumptions).