Coral reefs, the colourful rainforests of the ocean and home to a quarter of fish in the sea, seem doomed. Yet in the remote heart of the Indian Ocean lies a tiny group of islands that chance and biology have conspired to preserve in pristine, primal condition. They are as biologically significant as the Galápagos Islands or the Great Barrier Reef, bathed in seawater thought to be purer than any on the planet. The Chagos Islands offer a glimmer of hope for an ocean choking from man's impact. Best of all, they are administered by Britain. We have the golden opportunity to protect them.

The environmental elixir of the islands - otherwise known as the British Indian Ocean Territories - is lack of humans. A controversial resettlement 40 years ago to make way for a military base has spared them the tightening catastrophe that threatens life in the oceans. Absence of entrenched economic interests makes them relatively easy to protect.

In one of his last acts as President, George W. Bush used the US Antiquities Act to set aside 195,000 square miles of the Pacific as marine monuments, winning surprised gratitude from conservationists. In 2006 he did the same with 140,000 square miles around the northwest Hawaiian islands. His turnaround is largely thanks to a new scientific consensus that marine protected areas have near-miraculous powers for restoring the health of the seas.

The power of such reserves increases dramatically with size. Chagos offers the chance to protect 250,000 square miles of ocean with by far the richest biodiversity in British-controlled waters.

Marine life thrives in shallow and coastal water, so is forced into close contact with man: more than half the world's population lives within 100km of the sea. Unlike their Indian Ocean cousins, Mauritius, the Seychelles and the Maldives, the waters of Chagos have been spared the impact of development - sewage, fertiliser run-off, sedimentation, construction debris, not to mention fishing. In Chagos the livers of seabirds, usually host to the accumulated ills of a marine environment, show very low levels of toxic organic pollutants. The islands are so pure that scientists who visit go without sunscreen to avoid contaminating the water.

Coral forms the physical and biological heart of Chagos. The laval base of the islands rose from the seabed 45 million years ago as India crashed into Asia, creating the Himalayas. As the volcanic rock shrank back into the ocean the corals rose to form the world's largest remaining atoll. Beneath Diego Garcia, the largest of the 55 islands, the coral is a mile deep.

Coral species thrive here as nowhere else. In 1998 El Niño caused a spike in water temperatures that caused 80 per cent of the Indian Ocean's stony corals to bleach. Chagos rebounded faster than any known reef system. An important factor seems to be that the waters run so clear that coral life is most diverse at a depth of 20m - far deeper than normal and beneath the upper layers of water that warm fastest. Free from human impact, the reefs seem better able to resist the rising temperatures that threaten them.

Chagos is not only uniquely resilient, it is also a unique stronghold of biodiversity. DNA analysis of its corals by Professor Charles Sheppard, a marine scientist at Warwick University, shows that they form the centre of the Indian Ocean's genetic diversity. For scientists such as Sheppard, Chagos offers a baseline by which to judge the health of other ecosystems amid the effects of climate change. Its value will only increase.

The diversity of Chagos is not restricted to corals. A thousand species of fish teem around the islands; sharks, dolphins and turtles use them as a breeding ground. On shore, world-renowned birdlife is joined by 3ft wide crabs that climb trees to feast on coconuts.

The military base has proved remarkably compatible with the idea of a large-scale protected area. It keeps marauders at bay, and has surprisingly little impact on the environment. Alien species carried in ships' ballast water are one of the biggest threats to ocean biodiversity, but Diego Garcia's harbour is one of the few places in the world where surveys find not a single non-native species - indicating an ecosystem without man-made cracks where non-native species can take hold.

The conditions that have created this resilience and diversity are threatened by developers. Although most descendants of those evicted in 1965 appear reluctant to return, some are being encouraged to by people wishing to promote resettlement of the outlying islands as resorts.

There are no economic interests on the islands. Beyond a tiny coconut industry, tourism is the only possible income. Fishing licences worth about £1 million a year are sold, but this is exceeded by the cost of policing the 500,000 square miles of ocean. Every year Sri Lankan fishermen poach 500,000 tons of sea cucumber, and thousands of sharks die finless on the seabed.

Much of the total land area of the islands - all eight square miles of it - is set aside for bird sanctuaries. Small “no-take” marine zones have been designated but only 3 per cent of the shallow-water areas are protected, and almost none of the deeper seas. The islands' administration has discussed making the area a Unesco World Heritage Site, but this should be just a first step towards greater protection. A small facility should be established on Diego Garcia for research staff, rangers and conservation staff. Tightly controlled, ship-based tourism would ensure minimum impact. Funding could come from a trust. For such an iconic park, it should not be difficult to find.

The scientific consensus is that a third of the ocean must be protected from human pressures, and the bigger the continuous area the better. The history and location of the Chagos Islands has created a jewel of unsurpassed importance in the Indian Ocean. It is Britain's duty to protect it for future generations. It may be the only way our great-grandchildren can witness the wonder of a coral reef.

Frank Pope is ocean correspondent of The Times

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