In a concrete pen, basking in the warm equatorial sunshine, dozens of baby giant tortoises are about to make history. Later this year, these animals will be the stars in one of the boldest conservation initiatives ever attempted in the Galapagos, the best-preserved tropical archipelago left on earth.

Back in 1835, Charles Darwin marvelled at these extraordinary islands isolated in the midst of the Pacific. Today, as some 150,000 visitors experience a similar sense of wonder every year, the influence of Darwin is stronger than ever as conservationists tirelessly toil to maintain the subtle differences in the flora and fauna found on each of the islands in the archipelago. Just as they were for Darwin, these differences are a compelling illustration of evolution in action. They are what make the Galapagos special.

But now, after 50 years of enforcing strict segregation of the 11 or so recognised types of tortoise, keeping each contained on its own island or within its own volcano, conservationists are about to break with their purist past and take tortoises from one island, Española, and release them on to another, Pinta. This is the first time that conservationists in the Galapagos have attempted to replace one species with another, says Felipe Cruz of the Charles Darwin Research Station (CDRS), the institution on the central island of Santa Cruz that brings scientific know-how to the conservation effort.

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The reason for this introduction is simple. Pinta's tortoises are all but extinct. The only known individual – a hapless male called Lonesome George – has been in captivity at the CDRS since his discovery on the island in 1972. George was probably only one of few tortoises that survived the devastation wrought in the 18th and 19th centuries, by pirates and whalers in search of a square meal.

Without its tortoises, Pinta has suffered. In the 1950s, someone introduced a few goats to the island. They bred like billy-o, and within decades there were thousands crammed on to a volcano seven miles long and four miles wide. The Galapagos National Park Service (GNPS) responded with an armed assault. In the 1970s, wardens shot more than 40,000 of Pinta's goats, all descended from the few animals set down on the island little more than a decade earlier. Still, it was not until 2004 that the GNPS finally claimed victory against these mammalian aliens.

Since the eradication of Pinta's goats, the vegetation has bounced back. But in the absence of its dominant herbivore – the giant tortoise – the island's vegetation is at risk, says Ole Hamann, a botanist at the University of Copenhagen in Denmark, who has been studying Pinta's plants since the early 1970s. Some species are starting to crowd out others, he says: "Tortoises will open up the vegetation, making room for light-loving herbs and grasses."

The decision to replace one species with another – what's known as "taxon substitution" – is not without its risks. Some conservation biologists argue it's impossible to anticipate the consequences of such an intervention. "Many people like the idea of a pure Galapagos, the idea of finding a mate for Lonesome George and repopulating Pinta with pure-bred tortoises," says Bryan Milstead, head of vertebrate research at the CDRS. But right now there's also a need to manage the ecosystem properly. It's a tortoise-dominated, tortoise-evolved landscape. Pinta needs a dominant herbivore – now."

Conservationists in the Galapagos should be comforted by the experience of their counterparts in the Mascarenes and Seychelles in the Indian Ocean, the only places outside the Galapagos with wild giant tortoises. There, tortoises from the atoll of Aldabra have been used as replacements for extinct species. Returning tortoises to islands that once had them is good for ecological balance, says Justin Gerlach, scientific co-ordinator of the Nature Protection Trust of Seychelles. "As long as the habitat is well on the way to recovery I would have thought the Española tortoises will do well," he says.

This places the Galapagos and the Seychelles at the cutting edge of conservation biology, says Josh Donlan, a conservation biologist at Cornell University: "This should be replicated on islands around the world where suitable taxon substitutions exist and invasive mammals have been removed."

The individuals destined to fulfil this role are the offspring of a small group of Española tortoises brought to the CDRS in the 1970s. Since then, these animals – themselves the last of their kind – have produced more than 1,500 babies, which when old enough have been shipped to Española. With these offspring now grown up and breeding on their island, the GNPS can now send some of these captive-bred tortoises – which are Lonesome George's closest cousins – to Pinta.

The GNPS aims to introduce dozens of young Española tortoises to Pinta every year. They will be around five years old, and the size of a dinner plate – but this is too small for them to carry a satellite transponder. Most likely, however, they will be fitted with miniature solar-powered radio-transmitters. This should allow scientists to track the movements of each one, says Milstead, giving a unique insight into how tortoises colonise a new island and their impact on the vegetation.

The release was pencilled in for the first half of this year. But in January, park wardens on a routine visit to Pinta to check for goats made an unsettling discovery: the bloody massacre of dozens of sea lions. In all, they found the remains of 53 animals, including 13 pups, almost all of them with cranial fractures consistent with death by clubbing.

The last few years have seen increasing political and social stability in the islands and this episode has raised concerns that there is still a disgruntled minority prepared to sabotage the efforts of conservationists. The GNPS, however, is determined to push ahead with its plans to restore the ecological make-up of islands such as Pinta to something like their pre-human glory. So if all goes to plan and the Española tortoises are set free on Pinta later this year, will Lonesome George be amongst them? It's unlikely. Last year, geneticists produced the best news Lonesome George has received in more than 35 years in captivity: he may not be alone after all. A blood sample collected from a tortoise on Isabela Island in 2000 shows clear signs of Pinta ancestry. Unfortunately, the animal is also a male. Nevertheless, the geneticists and GNPS staff are planning an expedition to Isabela to see if they can track him down. There is always a chance he has sisters. If a suitable mate can be found and Lonesome George decided to breed, the radio signals emitted from the Española tortoises on Pinta could be used to round them up.

But time will not be on George's side. The Española tortoises heading towards Pinta should reach maturity in around 2020. Once they start breeding, it will be hard to deny that the substitution of Lonely George and perilous taxon is final.

To order a copy of Henry Nicholls' award-winning book Lonesome George, call Independent Books Direct on 08700 798897 or visit www.independentbooksdirect.co.uk