Canyonlands has completed a two-year effort to inventory Mexican spotted owls (Strix occidentalis lucida) within the park. The U.S. Fish and Wildlife Service federally listed the Mexican spotted owl as a threatened species in 1993. A significant area in Canyonlands has been designated as critical habitat for the Mexican spotted owl by the U.S. Fish and Wildlife Service. Canyonlands is considered one of the major population centers of the Mexican spotted owl on the Colorado Plateau.
Maine ocean islands provide the only nesting sites for Atlantic puffins in the United States. Eastern Egg Rock in the midcoast region, Seal Island and Matinicus Rock at the mouth of Penobscot Bay, and Machias Seal Island and Petit Manan Island off the downeast coast provide habitat for more than 4,000 puffins each summer.