But as scientists around the world prepare to celebrate the 200th anniversary of the great biologist's birth, the rich ecosystems he found 174 years ago on these islands off the coast of South America are now under threat of collapsing.
Conservation groups warn that invasive animals and insects introduced by visitors along with the rising number of tourists and permanent human inhabitants on the islands are destroying the rare endemic species that are found no where else in the world.
There are 106 species on the islands and in the surrounding waters, out of around 450, that are now considered endangered or critically endangered, while another 90 have been officially declared as vulnerable.
Of the 168 unique plants found no where else in the world, 60 per cent are close to extinction and in the past 10 years alone, at least three species, including a mouse that bore Darwin's name, have died out.
Scientists and conservation charities now fear that unless more is done to preserve the unique animals and plants that inhabit the islands, more species will be consigned to the history books.
Authorities on the islands are now drawing up strict new rules to restrict tourism and development on the islands.
"When Darwin visited the Galapagos, the number of animals would have been far greater," said Jonathan Rush, information manager at the Galapagos Conservation Trust. "The introduction of invasive species, tourism, fishing, development and pollution are the principal threats.
"The growing number of visitors has had an adverse impact and could destroy the islands if allowed to increase in an uncontrolled way."
Many of the iconic species that Darwin described during his visit to the Galapagos on HMS Beagle in 1835 are bearing the brunt of the losses.
Since his time there, three species of giant tortoise, among the most famous of the natural inhabitants, have disappeared.
Weighing up to 250kg and living for more than 100 years, there were 14 different species of giant tortoise on the Galapagos Islands, but settlers and passing sailors who captured the tortoises for food caused their numbers to dwindle from more than 100,000 to less than 15,000.
The most famous remaining giant tortoise is Lonesome George, the last surviving Pinta Island giant tortoise. When he dies a fifth species of giant tortoise will have become extinct.
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David Robinson, a senior lecturer in life sciences at the Open University and academic adviser for the BBC who has visited the islands on many occasions, said: "When Darwin arrived on the islands he commented on how he was unable to find anywhere to pitch his tent due to the number of burrows made by the land iguanas that lived there. When I was there you could barely find any."
The famous finches on the Galapagos Islands, nicknamed Darwin's finches after he used their varying beak size on different islands as an example of his theory of natural selection, are also suffering.
Since 1991 tourist numbers have soared from 41,000 to more than 160,000 annually, while the local population has grown by four per cent every year to reach more than 40,000.
Recent research has revealed that this growing human presence is causing the evolution of some of the species to go into reverse. They found variation in beak size was decreasing in the medium ground finch when living near to humans.
Insects and animals introduced to the islands by humans are also destroying the diversity. There are now 748 introduced species of plants compared with 500 native plant species.
At least 490 species of insect and 53 other invertebrates have been introduced to the Galapagos, 55 of which are known to be severely impacting the native species. A parasitic fly Philornis downsi is one example that is attacking Darwin's finches.
Black rats, that arrived on the islands as stowaways on ships, have been responsible for eating bird eggs, destroying nests and competing with native rodents such as Darwin's Galapagos mouse, declared extinct in 1996, and the Indefatigable Galapagos mouse, found to be extinct in 2000.
Four species of bird, including the Mangrove finch, Galapagos petrel and the Galapagos albatross, are now critically endangered. There are between 18 and 30 Floreana mockingbirds, which particularly caught Darwin's eye, left, making them one of the rarest birds in the world.
There are also just 1,538 Galapagos penguins, the only species of penguin found north of the Equator. A form of avian malaria is ravaging the birds while changes in climate and predation from cats has reduced their population further.
Feral goats and pigs that were introduced to the islands by whalers have caused extensive damage to the delicate ecosystems. Conservation groups have now managed to eradicate goats from seven of the nine main islands.
Visitors to uninhabited islands must all now be accompanied by park rangers, are banned from carrying food and must completely change their clothing to avoid carrying seeds ashore.
Professor Steve Jones, an evolutionary geneticist at University College London, said: "On the Galapagos, goats and cats are a plague, pigeons have pushed out their feathered relatives and alien wasps have done terrible damage to the insects. The islands face an era in which specialists, evolved to fit their own small place in nature, have fallen to loutish strangers able to cope more or less anywhere."