The Galápagos were discovered by chance in March 10, 1535 when Dominican Fray Tomás de Berlanga, the Bishop of Panama, sailed to Peru to settle a dispute between Francisco Pizarro and his lieutenants after the conquest of the Incas, while performing an administrative mission for the Spanish Monarch Carlos V. The bishop's ship stalled when the winds died and strong currents carried him out to the Galápagos. The islands first appeared on maps in about 1570 in those drawn by Abraham Ortelius and Mercator

Ecuador annexed the Galápagos Islands on February 12, 1832, naming it Archipelago of Ecuador. 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.

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.

Over the course of a whole year, from September 1904, an expedition of the Academy of Sciences of California, led by Rollo Beck, stayed in the Galápagos collecting scientific material on geology, entomology, ornithology, botany, zoology and herpetology. Another expedition from that Academy was done in 1932 (Templeton Crocker Expedition) to collect insects, fish, shells, fossils, birds and plants.

During WWII Ecuador authorized the United States to establish a naval base in Baltra island and radar stations in other strategic locations.

In 1946 a penal colony was established in Isabela Island, but was suspended in 1959.