The Michigan Islands Wilderness now contains a total of 12 acres and is managed by the Fish & Wildlife Service. All of the Wilderness is in the state of Michigan. In 1970 the Michigan Islands Wilderness became part of the now over 110 million acre National Wilderness Preservation System.

Eight small islands in Lakes Huron and Michigan were established as Michigan Islands National Wildlife Refuge in 1943, and three of these islands have been designated Wilderness: Pismire, Scarecrow, and Shoe. At seven acres, Scarecrow Island is the largest of the three Wilderness isles, which together form one of the smallest units of the National Wilderness Preservation System. Large submerged limestone shoals located offshore protect a shoreline of rock and cobble. Several colonial bird species - great blue heron, black-crowned night-heron, herring gull, ring-billed gull, great black-backed gull, common tern, Caspian tern, and double-crested cormorant - nest on these islands in substantial numbers. Standing dead green ash trees are the main vegetation, with a lush understory of common elderberry, scattered red-osier dogwood, and an abundance of "weedy" plants. The death of the ash has been blamed on the extensive use by cormorants. In order to protect nesting birds, public visitation is prohibited.

Michigan Islands National Wildlife Refuge, including the Designated Wilderness, is closed to public access except by special use permit or for maritime emergencies.