Understanding ecological boundaries is recognized by ecologists as important for understanding ecosystem dynamics. All borders are borders in relation to some organism. However, much of the literature on habitat change ignores this basic ecological fact. In addition, borders are highly influenced by accidental or historical features of ecosystems, and researchers have in many cases defined them only in terms of convenience. Several viewpoints explored in this article reflect this skepticism about identifying ecosystems as real structured entities. I draw on Ghiselin’s (...) hypothesis that species are not natural kinds but individuals, to develop a relational approach to ecological boundaries. I argue that with regard to ecology a border is always a border for a specific organism, and is a border in a specific manner for that organism. I draw on studies of two species of tsetse fly found in the Mauhoun river basin in Burkina Faso to illustrate why this relational approach is important. This approach may also help identify weaknesses in conservation efforts that have not properly asked the question, “Boundary for what?”. (shrink)