During the 19th century Spain 's power in Latin America began to decline. The countries of South America began trading independently with England and France , and the heyday of the Pirate drew to a close. The industrial revolution had changed the world, and now rather than Spanish gold, seafarers were in search of oil. Oil came in the form of whale blubber.

By 1792, British whalers reached the Galapagos and began to hunt the mighty creatures. The upwelling in the islands made the Galapagos an excellent feeding ground for whales and the Islands of Isabela and Fernandina were a favorite calving place of whales.

Between the years of 1811 and 1844 it is thought some 700 whaling ships visited these islands. Whaling was a lucrative business, with very few regulations. Damage to the Galapagos environment by the whalers was unprecedented. Each whaling ship would collect between 500-600 tortoises to provide fresh meat on the cruise. It is estimated that whaling ships removed 15,000 tortoises from Floreana causing the extinction of that subspecies as well as those on Santa Fe and Rabida. In total it is thought that Whalers removed some 200,000 tortoises from the Galapagos. The whalers also created problems that would long survive them; they introduced a number of animals to the Galapagos including the black rat, cats, cattle, donkeys, goats and dogs.

A famous whaler who visited the Galapagos was author Herman Melville who wrote about his visit to the islands in the story, The Encantadas . By 1835 Whaling visits to the Galapagos ended, and by 1859 with the discovery of the first commercial scale petroleum (a less expensive form of oil) whaling quickly declined throughout the world.