By the mid-nineteenth century, guano phosphate had become the miracle fertilizer of American agriculture. In 1856, Congress passed the Guano Islands Act, authorizing U.S. citizens to claim uninhabited islands rich in the stuff. Sea captain Peter Duncan did exactly that on September 19, 1857, staking Navassa for the United States. Haiti protested immediately, pointing to constitutional claims stretching back to 1801. President James Buchanan responded with an executive order and the threat of military force. The Navassa Phosphate Company of Baltimore soon arrived with dynamite, pick-axes, and rail cars. They built barracks for 140 Black contract laborers from Maryland, houses for white supervisors, a blacksmith shop, and a church at Lulu Bay. Mining began in 1865, and for the next three decades workers hauled guano through brutal tropical heat to load onto the company barque, the S.S. Romance.

The conditions were as harsh as the name Romance was ironic. In 1889, simmering rage over the treatment of laborers erupted into a full-scale riot that left five supervisors dead. A U.S. warship carried eighteen workers back to Baltimore to face murder charges in federal court. The Order of Galilean Fishermen, a Black fraternal society, raised funds for the defense. E. J. Waring, the first Black lawyer admitted to the Maryland bar, joined the legal team and argued that the United States had no jurisdiction over the island at all. The case, Jones v. United States, reached the Supreme Court in October 1890, which ruled the Guano Act constitutional. Three miners were sentenced to death. But a grassroots petition, driven by Black churches across the country and signed even by white jurors from the trials, reached President Benjamin Harrison. He raised the case in his 1891 State of the Union Address, and the sentences were commuted. Mining resumed, though at a much-reduced scale.

The Spanish-American War in 1898 finally forced the Phosphate Company to abandon Navassa. Haitians briefly occupied the island and seized the company's remaining assets, though they could not operate the machinery. The company went bankrupt, and Navassa fell quiet. When the Panama Canal opened in 1914, shipping traffic through the Windward Passage surged, and the little island became a navigational hazard. Congress appropriated $125,000, and in 1917 the U.S. Lighthouse Service erected a 162-foot lighthouse atop the island, 395 feet above sea level. A keeper and two assistants lived on Navassa until an automatic beacon replaced them in 1929. The U.S. Navy posted an observation crew during World War II. After that, human habitation ended for good.

In 1999, the U.S. Fish and Wildlife Service established the Navassa Island National Wildlife Refuge, encompassing 1,344 acres of land and a twelve-nautical-mile radius of surrounding marine habitat. The island shelters eight species of native reptiles, all believed to be endemic, though three are now likely extinct, including a subspecies of the rhinoceros iguana and a dwarf boa. Four species of trees form a low canopy over the coral terrain: short-leaf fig, pigeon plum, mastic, and poisonwood. Offshore, elkhorn coral was found in good condition in 2012. BirdLife International designated Navassa an Important Bird Area for its breeding colonies of red-footed boobies, magnificent frigatebirds, and hundreds of white-crowned pigeons. The refuge is closed to the general public. Transient Haitian fishermen still work the surrounding waters, but no one calls the island home.

The territorial dispute remains unresolved. Haiti has named Navassa explicitly in its constitution since 1874. The United States administers it through the Fish and Wildlife Service. Cuba backs Haiti's claim. The standoff has prevented the definitive delimitation of maritime boundaries between four nations. Amateur radio operators, who visit occasionally with Fish and Wildlife Service permission, know the island by its call sign prefix KP1, and one operation designated K1N logged 138,409 contacts from its shores. Navassa remains what it has always been: a place people fight over but rarely choose to stay.