Ecosystem boundaries are zones of transitions between two adjacent habitats. They occur naturally in all biomes but the extent of boundaries has been greatly increased by anthropogenic habitat modification. Transition zones are characterized by a profound change in the composition of plant and animal communities and that transition may be abrupt, gradual or even occur via a series of intermediate habitat types. Naturally occurring ecosystem boundaries sometimes form a unique habitat to which species are specifically adapted, whereas anthropogenically created ecosystem boundaries typically contain a mixture of species from the two adjacent ecosystems and often exert a negative influence on natural habitats. Adjacent ecosystems are connected via flows of energy, material and organisms across ecosystem boundaries, and these flows can exert strong influences on the fertility and productivity of ecosystems. The magnitude of cross‐system fluxes is mediated by a wide range of variables. Key concepts: Ecosystem boundaries are the locations exhibiting gradients of change in environmental conditions and a related shift in the composition of plant and/or animal communities. Naturally occurring ecosystem boundaries can represent unique habitats to which many species are specifically adapted. Anthropogenically created ecosystem boundaries often support high species diversity, but the combination of species present at edges is very different to the one found deep inside the adjacent ecosystems. Neighbouring ecosystems experience flows of organisms, materials and energy across the shared boundary.