The islands are part of the Islas de la Bahía y Cayos Cochinos Important Bird Area (IBA), designated as such by BirdLife International because they support significant populations of white-crowned pigeons, chimney swifts and yellow-naped amazons.

[4] The Swan Islands were discovered by Christopher Columbus in 1502 and named the Islas de las Pozas.

Messers Sterns, Fabens, and Green incorporated the Atlantic and Pacific Guano Company, which issued 50,000 shares at a price of $100 each for a total capitalization of $5,000,000 in 1858.

[6] The company even issued currency, signed by William H. Whitfield, in 25-cent, 50-cent, and one-dollar denominations on June 1, 1867, to facilitate commerce on the islands.

The islands gained notoriety in the early 1960s from the activities of Radio Swan, which began broadcasting in May 1960 during the preparation for and, later, the conduct of the Bay of Pigs Invasion of Cuba.

The group, called the Kononiers, had been in existence for about five years, the student told the newspaper, and was armed through a series of burglaries of the Deep River Armory store.

[10] In 1987, the Los Angeles Times reported that the CIA and other American governmental agencies had a covert training facility on Swan Island for Nicaraguan Contras.

Luxury real estate and hotels, valued at five billion dollars, were envisioned, with a main city named Cygnet.

In July 2023, President Xiomara Castro of Honduras announced plans to build an isolated prison on the island for up to 2,000 gang leaders.