The island of Desecheo is located 14 miles west of Puerto Rico and is bounded by the Atlantic Ocean on the north and the Caribbean Sea on the south. The refuge encompasses the entire rugged island. From 1940 to 1952 the island was used as a practice target for aerial bombardment by the US War Department and from 1952 to 1960 Desecheo was used as a survival training area for the U.S. Air Force. Although formerly containing a colony of 15,000 brown boobies and 10,000 red-footed boobies, currently no successful booby breeding is known to occur on the island.

Other seabird species also use the island. There are three endemic species of lizards. An endangered cactus is found on the island and hawksbillturtles sometimes nest on the refuge. Feral goats became established on the island in the 1700's. Nopublic use is allowed on the island because of safety considerations associated with unexploded ordnance that remain on the refuge. The refuge has had a colorful past. In 1966, the National Institutes of Health introduced 56 rhesus monkeys to be later culled for medical research. Desecheo is often used as a drop off point for illegal aliens and drugs.