European discovery of the Galápagos Islands occurred when Spaniard 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 10 March 1535. According to a 1952 study by Thor Heyerdahl and Arne Skjølsvold, remains of potsherds and other artifacts from several sites on the islands suggest visitation by South American peoples prior to the arrival of the Spanish. However, no remains of graves, ceremonial vessels and constructions have ever been found, suggesting no permanent settlement occurred at the time.
The Galápagos Islands first appeared on the maps, of Gerardus Mercator and Abraham Ortelius, in about 1570. The islands were named "Insulae de los Galopegos" (Islands of the Tortoises) in reference to the giant tortoises found there.
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.
In 1793, James Colnett described the flora and fauna of Galápagos, and suggested the islands could be used as base for the whalers operating in the Pacific Ocean. He drew the first accurate navigation charts of the islands.
The first known permanent human resident on Galapagos was Patrick Watkins, an Irish sailor who was marooned on the Island Floreana from 1807–1809. According to later accounts, Watkins managed to survive by hunting, growing vegetables and trading with visiting whalers, before finally stealing an open boat and navigating to Guayaquil.
Ecuador annexed the Galápagos Islands on 12 February 1832, naming them the Archipelago of Ecuador. This new name 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 them.
The voyage of the Beagle brought the survey ship HMS Beagle, under captain Robert Fitzroy, to the Galápagos on 15 September 1835 to survey approaches to harbors. The captain and others on board, including his companion, the young naturalist Charles Darwin, made observations on the geology and biology on Chatham, Charles, Albemarle and James islands before they left on 20 October to continue on their round-the-world expedition. Primarily a geologist at the time, Darwin was impressed by the quantity of volcanic craters they saw, later referring to the archipelago as "that land of craters". His study of several volcanic formations over the 5 weeks he stayed in the islands, led to several important geological discoveries, including the first, correct explanation for how volcanic tuff is formed. Darwin noticed the mockingbirds differed between islands, though he thought the birds now known as Darwin's finches were unrelated to each other, and did not bother labeling 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 Darwin the 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 analyzed on his return to England, it was found that many apparently different kinds of birds were species of finches, which were 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.