The Piping Plover is a threatened species that nests on Assateague.
In 2001 and 2002, the homeowners' association commissioned a survey of endangered plants and animals on the island, some of the animals of special interest were piping plovers, sea turtles, sea beach amaranth, and marine mammals.
Various levels of government are undertaking a process to create the territory as an historical site and conservation area for the numerous species of migratory birds which inhabit the island during the summer months; these include Piping Plovers, with the Sandy Point colony comprising between 15-30% of Newfoundland's overall plover population.
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The Refuge provides crucial habitat for many different types of endangered or threatened birds, including the American Bald Eagle, Peregrine Falcon, American Black Duck, and the Piping Plover.
The refuge is an important staging area for migratory birds, and is used as well for the management and study of endangered species such as the Northeastern Beach Tiger Beetle and Piping Plover.