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Land management agencies need to plan and prioritize their activities to best use limited resources. To implement ecosystem management, the US Fish and Wildlife Service has defined watershed-based planning units, such as the Mississippi Headwaters/Tallgrass Prairie Ecosystem. To identify important habitats for migratory birds in this ecosystem, we ranked habitats according to their importance for breeding birds of conservation concern, using rankings of the birds' conservation priority within this ecosystem. Grasslands and wetlands were the highest ranked habitats because 12 (46%) and 9 (25%), respectively, of the species breeding in these habitats had "Partners in Flight" scores greater than 19 (maximum 35). Shrub-sapling stands and lake habitats ranked next, and forest habitats ranked lowest. The four highly ranked habitats are widespread in the Great Plains. These habitats can contribute to the conservation of a variety of high-priority bird species, if the habitats are restored and managed for birds.