March 1535: The Galapagos Islands are discovered...accidentally, by the Bishop Tomás de Berlanga
Ecuador annexed the Galápagos Islands on February 12, 1832, naming it Fray Tomás de Berlanga, the fourth Bishop of Panama, sailed to Peru to settle a dispute between Francisco Pizarro and his lieutenants. De Berlanga's vessel drifted off course when the winds diminished, and his party reached the islands on March 10, 1535. According to a 1952 study by Thor Heyerdahl and Arne Skjølsvold, remains of potshards and other artifacts from several sites on the islands suggest visitation by South American peoples prior to the arrival of the Spanish.

The islands first appeared on maps in about 1570 in those drawn by Abraham Ortelius and Mercator. The islands were called "Insulae de los Galopegos" (Islands of the Tortoises).

The first English captain to visit the Galápagos Islands was Richard Hawkins, in 1593. Until the early 19th century, the archipelago was often used as a hideout by mostly English pirates who pilfered Spanish galleons carrying gold and silver from South America to Spain.

Alexander Selkirk, whose adventures in Juan Fernández Islands inspired Daniel Defoe to write Robinson Crusoe, visited the Galápagos in 1708 after he was picked up from Juan Fernández by the privateer Woodes Rogers. Rogers was refitting his ships in the islands after sacking Guayaquil.

The first scientific mission to the Galápagos arrived in 1790 under the leadership of Alessandro Malaspina, a Sicilian captain whose expedition was sponsored by the King of Spain. However, the records of the expedition were lost.

In 1793, James Colnett made a description of the flora and fauna of Galápagos and suggested that the islands could be used as base for the whalers operating in the Pacific Ocean. He also drew the first accurate navigation charts of the islands. Archipelago of Ecuador. This was a new name that added to several names that had been, and are still, used to refer to the archipelago. The first governor of Galápagos, General José de Villamil, brought a group of convicts to populate the island of Floreana and in October 1832 some artisans and farmers joined.

The voyage of the Beagle brought the survey ship HMS Beagle under captain Robert FitzRoy to the Galápagos on September 15, 1835 to survey approaches to harbors. The captain and others on board including his companion the young naturalist Charles Darwin made a scientific study of geology and biology on Chatham, Charles, Albemarle and James islands before they left on October 20 to continue on their round-the-world expedition. Darwin noticed that mockingbirds differed between islands, though he thought the birds now known as Darwin's finches were unrelated to each other and did not bother labelling them by island. The Englishman Nicolas Lawson, acting Governor of Galápagos for the Republic of the Equator, met them on Charles Island and as they walked to the prison colony told him that tortoises differed from island to island. Towards the end of the voyage Darwin speculated that the distribution of the mockingbirds and the tortoises might "undermine the stability of Species". When specimens of birds were analysed on his return to England it was found that many apparently different kinds of birds were species of finches which were also unique to islands. These facts were crucial in Darwin's development of his theory of natural selection explaining evolution, which was presented in The Origin of Species.

José Valdizán and Manuel Julián Cobos tried a new colonization, beginning the exploitation of a type of lichen found in the islands (Roccella portentosa) used as a coloring agent. After the assassination of Valdizán by some of his workers, Cobos brought from the continent a group of more than a hundred workers to San Cristóbal island and tried his luck at planting sugar cane. He ruled in his plantation with an iron hand which lead to his assassination in 1904. Since 1897 Antonio Gil began another plantation in Isabela island.

During World War II Ecuador authorized the United States to establish a naval base in Baltra island and radar stations in other strategic locations. Baltra was also established as a US Air Force Base at this time. Crews stationed at Baltra patrolled the Pacific for enemy submarines as well as providing protection for the Panama Canal. After the war the facilities were given to the government of Ecuador. Today the island continues as an official Ecuadorian military base. The foundations and other remains of the US base can still be seen as one crosses the island. In 1946 a penal colony was established in Isabela Island, but it was suspended in 1959. The Galapagos became a national park in 1959 and tourism started in the 1960s.