In most human conflicts, there are good guys and bad guys. This is not so in the history of global conservation, which is at least partly a story of good guy versus good guy. The major contestants in the struggle to protect nature and preserve biological diversity may seem to be transnational conservation organisations on one side and rapacious extractive industries on the other. But there is a larger, more lamentable conflict: the one between transnational conservation and the worldwide movement of indigenous peoples - good guys both.

These two forces share a goal that is vital to life on earth - a healthy and diverse biosphere. Both are communities of integrity led by some of the most admirable, dedicated people alive. Both care deeply for the planet and together are capable of preserving more biodiversity than any other two groups on it. Yet they have been terribly at odds with one another over the past century or more, violently so at times, mostly because of conflicting views of nature, radically different definitions of "wilderness" and profound misunderstandings of one another's science and culture.

The perceived arrogance of "big conservation" is a confounding factor; so too is the understandable tendency of some indigenous people to conflate conservation with imperialism. The results of this century-old conflict are thousands of protected areas that cannot be managed and an intractable debate over who holds the key to successful conservation in the most biologically rich areas of the world.

Violent effort

The conflict began in the bucolic stillness of Yosemite valley in the eastern Sierra Nevada mountains of California. From the middle of the 19th century until 1914, when Yosemite became a national park, a concerted and at times violent effort was made to rid Yosemite of its natives, a small band of Miwok Native Americans who had settled in the valley about 4,000 years ago.

During the same period, most of the major parks created in America - notably Yellowstone, Grand Canyon, Mesa Verde, Mount Rainier, Zion, Glacier, Everglades and Olympic - repeated the Yosemite example by expelling thousands of tribal people from their homes and hunting grounds so that the new parks could remain in a "state of nature". This practice of conservation was exported worldwide, becoming known as "the Yosemite model". Refugees from conservation areas have never been counted; they are not even officially recognised as refugees. But the number of people displaced from traditional homelands worldwide over the past century in the interest of conservation is estimated to be close to 20 million, 14 million of them in Africa alone.

I have travelled across all five inhabited continents researching this subject, visiting hundreds of indigenous communities, some in conflict with western-style conservation, others in harmony with it. Although tension persists, along with arrogance, ignorance and the conflicts they breed, I found an encouraging dialogue growing between formally educated wildlife biologists, who once saw humanity as inimical to nature, and ancient aboriginal societies that have passed their remarkable ecological knowledge from generation to generation without a page of text. I found, mostly in the field, a new generation of conservationists who realise that the very landscapes they seek to protect owe their high biodiversity to the practices of the people who have lived there, in some cases for thousands of years.

Wildland conservation has a recorded history and a literary tradition. Aborigines evicted from their homelands in the interest of conservation have only memory and the bitter oral narrative I heard again and again while visiting their makeshift villages and refugee camps; their pre-eviction experience is rarely recorded outside the literature of anthropology. So the concept of "fortress conservation" and the preference for "virgin" wilderness has lingered in a movement that has tended to value all nature but human nature, and refused to recognise the positive wildness in human beings.

Thus the beautifully written and widely read essays and memoirs of early American eco-heroes such as John Muir, Lafayette Bunnell, Samuel Bowles, George Perkins Marsh and Aldo Leopold inform a conservation mythology that until quite recently separated nature from culture and portrayed both natives and early settlers of frontier areas as reckless abusers of nature, with no sense or tradition of stewardship, no understanding of wildlife biology and no appreciation of biodiversity.

It was the "manifest destiny" of conservation leaders, then, to tame what the 17th-century Massachusetts Puritan poet and minister Michael Wigglesworth described as

A waste and howling wilderness / Where none inhabited / But hellish fiends, and brutish men / That devils worshipped

It has taken transnational conservation a century to see the folly of some of its heroes, such as Richard Leakey, who recently denied the existence of indigenous peoples in his home country, Kenya, and called for the removal of all "settlers" from game reserves and other protected areas.

Today, all but the most stubborn enclose-and-exclude conservationists are willing to admit that it is specious to conflate nature with wilderness and occupants with "first visitors". They have recognised that indigenous people manage immense areas of biologically rich land, even if they don't own it. And most, although not all, are managing it well.

Hostile evictees

Some conservationists argue that a policy of tolerating the impoverishment of indigenous people has wrecked the lives of 20 million poor, powerless but eco-wise people, and has been an enormous mistake - not only a moral, social, philosophical and economic mistake, but an ecological one as well. For it is far better to have good stewards living on land than to have that same land cleared of residents and surrounded by hostile evictees. Enlightened conservationists are beginning to accept the axiom that only by preserving cultural diversity can biological diversity be protected, and vice versa.

As conservationists and native people make their uneasy convergence, I hope they will come to agree that they both own the interdependent causes of biodiversity conservation and cultural survival, that they need each other, and that together they can create a new conservation paradigm that honours and respects the ways of life of people who have been living sustainably for generations on what can only be fairly regarded as their native land.

And I hope that native people will blend their traditional knowledge systems with the newer sciences of ecology and conservation biology in search of better ways to preserve the diversity of species , which is not only vital to their own security but to all life on earth. At this point, as the entire planet seems poised to tip into ecological chaos, with almost 40,000 plant and animal species facing extinction and 60% of the ecosystem services that support life failing, there may be no other way.

• Mark Dowie's latest book is Conservation Refugees: The Hundred-Year Conflict Between Global Conservation and Native Peoples, published by MIT Press, priced £18.99. To order a copy for £17.99 plus p&p, call 0330 333 6846 or go to theguardian.com/bookshop