The extraordinary wildlife on the remote islands off the coast of Ecuador inspired Darwin to develop his ideas on how different animals are moulded by the environment and ultimately his ideas on the origin of mankind.
However, 200 years since the great biologist's birth, it is mankind that is threatening the island with the introduction of invasive species, the demands of a growing human population, extreme weather events caused by climate change and a growing number of tourists disturbing the pristine wildlife.
Andrew Marr, the broadcaster and President of the Galapagos Conservation Trust, said development must be brought under control to protect the remaining species, with tourists limited to one visit to the islands during a lifetime.
Sir David Attenborough argued that tourists are a "necessary evil", providing income to natives of the island, but agreed development of hotels and transport links must be sustainable.
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.
Speaking at a dinner at Christ's College, Cambridge, to mark the 200th anniversary of Darwin's birth, Mr Marr warned that the islands' habitats face ruination unless human development leaves space for the wildlife.
Mr Marr first visited the islands to research Darwin as part of the BBC's Great Britons series and has since become an advocate of the World Heritage Site.
But he said visits, that are already controlled by the Galapagos National Park, should be limited to once in a lifetime.
"The Galapagos islands are truly astonishing – home to many unique species," he said.
"But they are very delicate, and there is huge pressure on them because of tourism, development and the introduction of invasive species. That is why, having been to the islands once, I promise never to go back."
Charles Darwin found a host of unusual animals on his visit to the archipelago on the HMS Beagle in 1835, including the famous giant tortoises.
But he also brought the first invasive insects and animals that have gradually been eroding the natural flora and fauna ever since.
Black rats and goats have been particularly damaging to the environment but perhaps the most invasive species of all are humans.
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. Some species of the giant tortoise and the Galapagos mouse have disappeared completely.
Sir David Attenborough, who is also due to speak at the dinner, last visited the Galapagos Islands on his 80th birthday.
Writing in this month's Lonely Planet Magazine, he described tourism as a "necessary evil" that is providing income to the islanders and conservation but must be controlled.
"We can screw up the Galapagos in the way that we can very easily screw up the whole planet," he warned. "These islands are an example, a parable, for how we treat the natural world."
Events around the country today are due to celebrate the birth of Charles Darwin. HRH the Duke of Edinburgh is due to unveil a new statue of Darwin at Christ's College and a series of free public events are being held at the Natural History Museum in London.
Toni Darton, Chief Executive of the Galapagos Conservation Trust, hoped the celebrations will help to boost funding for the huge amount of conservation work needed to ensure the species Darwin studied can survive another 200 years.
"Darwin helped to put the Galapagos on the map and now the huge interest in Darwin and the anniversary of his birth could ensure the islands' survival," she said.
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