Migratory movements of animals frequently span political borders and the need for international collaboration in the conservation of migratory species is well recognized. There is, however, less appreciation of the need for coordinated protection within nations. We explore consequences of multilevel governance for top-down implementation of international agreements, drawing on examples from Australia and with reference to the United States and European Union. Coherent implementation of legislation and policy for migratory species can be challenging in federal jurisdictions where environmental law making can be split across multiple levels of governance and local and federal priorities may not necessarily be aligned. As a result of these challenges, for example, two-thirds of Australian migratory birds remain unprotected under national legislation. In Australia and elsewhere, coordinated protection of migratory species can be implemented within the current framework of conservation law and policy by actions such as designating national migration areas, negotiating nationally coordinated agreements or listings of migratory species and pursuing new bilateral agreements with key countries along migratory routes.