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Within the last 20 years, the US has mounted a massive campaign against invasions by non-indigenous species (NIS) such as zebra mussels, kudzu, water hyacinths, and brown tree snakes. NIS have disrupted native ecosystems and caused hundreds of billions of dollars of annual damage. Many in the scientific community say the problem of NIS is primarily political and economic: getting governments to regulate powerful vested interests that introduce species through such vehicles as ships’ ballast water. This paper argues that, although politics and economics play a role, the problem is primarily one of scientific method. Even if commercial interests were willing to spend the necessary funds to control NIS, and even if government were willing to regulate them, ecological theory is not adequate to provide clear direction for either effort. The paper argues there is no comprehensive, predictive “theory of invasibility,” as part of a larger theory of community structure, that might guide ecological decision making regarding NIS, and for at least three reasons. (1) There is no firm definition of “NIS,” “native,” “exotic,” and so on, and ecologists do not use the terms consistently; as a result, biologists debating various accounts of community structure and ecological explanation often do not even make logical contact with each other. (2) The dominant theory used to understand invasibility, island biogeography, has no precise predictive power and is unable to clarify when NIS might promote biodiversity and when they might hinder it. (3) There are no firm, empirical generalizations that reveal when a colonizer or a NIS might be likely to take over a new environment, and when it might not succeed in doing so. As a result, scientists have only rough “rules of thumb” to shore up their arguments against NIS. Given the incompleteness of current ecological theory, the paper closes with several suggestions for ways that study of NIS might enhance understanding of basic commmunity structures and vice versa.