Marina Silva will never forget the day the bulldozers rolled up on her family's doorstep. It was the beginning of the 1970s and in the isolated Amazon community of Bagaço, where she was born, Silva, then about 12, looked on curiously as work began on a major highway to link the Brazilian rainforest with the rest of the country. Shortly afterwards, her relatives began to die. First two younger sisters, then her uncle and finally her cousin: all victims of a malaria epidemic imported by the road builders.

"I don't know if I was conscious that the road was bringing all that, but it made me write on my own flesh the consequences of what it meant to mess around with nature without giving the slightest attention to the need to look after it," she remembers.

Fast-forward to January 2003. Following the historic election of Brazil's first working-class president, Luiz Inácio Lula da Silva, Marina Silva was named the environment minister of South America's largest country, thrusting this former rubber tapper, who was virtually illiterate until her teens, on to the front line of Brazil's battle against deforestation - and of the global fight against climate change. Environmental groups rejoiced at her nomination. She was a woman from the forest, who understood the dangers inherent in destroying it.

Last Tuesday, however, the fairytale came to an abrupt end. After just over five years as environment minister, Silva resigned following a succession of acrimonious disputes with fellow ministers and businessmen who accused her of stalling major development projects in the Amazon and hindering the Brazilian economy. In her short resignation letter, Silva cited "the growing resistance found by our team in important sectors of the government and society".

The same groups that had heralded Silva's rise to power immediately opened fire on the government. "It's time to start praying [for the rainforest]," said Sergio Leitao, the director of public policy for Greenpeace in Brazil, claiming the government had "now made it clear that the idea of development at any cost is what will win out". Lula responded by insisting that his government would not stray from its quest to protect the Amazon and appointed another high-profile environmentalist, Green party founder Carlos Minc, as his new minister.

But aside from Silva's numerous enemies in the world of agri-business, few believe her departure bodes well for the future of the world's largest tropical rainforest. So why did she walk away? And what does her dramatic exit mean for the future of the Brazilian Amazon and, indeed, for the rest of the world?

On Tuesday, exactly a week after her resignation, a weary-looking Silva, 50, is unable to pinpoint a single cause for her decision. "Throughout these five years I faced numerous moments of great tension but they did not mean that the actions I was implementing lost strength," she says. However, last week the situation changed. "At this moment, in my perception, I had lost the strength to carry on doing these things."

Silva is officially between jobs (she will return to her seat in the senate at the end of the month), but in her third-floor apartment in the capital, Brasilia, surrounded by half a dozen giant, multicoloured orchids sent by well-wishers, she looks as busy as ever. She clutches a handful of documents, eyeing them repeatedly between questions. She is careful not to name names but leaves little doubt as to why she abandoned the government of Lula, a longtime friend and ally from Brazil's Workers Party.

"I realised that I was no longer in a position to stabilise what had already been achieved and to carry on expanding these achievements," she says baldly. Seven days after resigning, she has still not seen the president, whom she has known for 30 years.

Silva's resignation is the story of a conflict between two very different Brazils. In one corner are the farmers, businessmen and ordinary Brazilians who see the country's vast natural resources as a sure route to economic success. In the other are the environmental activists, indigenous groups and concerned spectators who believe that Brazil's march to economic greatness will mean the continued devastation of its rainforest and its peoples. Silva attempted to tread a path between the two visions, trumpeting the idea of sustainable development. This, she said, would provide better living conditions for the 25 million people in the Amazon region without obliterating the rainforest itself.

"There is no longer a way of thinking about growth for growth's sake," she argues. "Growth is important, but it needs to be growth with development and sustainability, in all of its senses: social, environmental, economic, cultural."

But walking this tightrope was never going to be simple, even for the notoriously resilient Silva, who frequently cites Nelson Mandela as one of her inspirations.

Maria Osmarina da Silva was born in 1958 in a community of rubber tappers called Seringal Bagaço, deep in the western state of Acre, not far from the border with Bolivia. The nickname Marina stuck immediately. One of 11 children (three later died), she was orphaned at 16 and moved to the state capital Rio Branco. Here she received a Catholic education and worked as a household maid to make ends meet.

Heavily influenced by liberation theology, she graduated in history from Acre's Federal University at 26 and became increasingly politically active. In 1984 she helped create Acre's first workers' union.

From an early age Silva was considered a guerreira, a battler, overcoming numerous episodes of tropical diseases such as malaria, and later mercury poisoning. At 35, she was elected as the youngest female senator in Brazil's history. She became a household name, famous for her shrill but powerful voice and unflinching defence of the Amazon. She converted to evangelism and in 1994 became a missionary for the Pentecostal church God's Assembly. She also gained growing international exposure, winning a succession of awards for her environmental work. When Lula da Silva was piecing together his first cabinet, her name was reportedly top of his list.

It was a crucial moment: between 2001 and 2002, 26,000sq km (10,000 sq miles) of rainforest had been lost. Illegal logging was spiralling out of control. A 40-year assault, led by an unholy trinity of loggers, ranchers and, more recently, soy farmers, had destroyed an estimated 20% of the Brazilian Amazon.

In August last year, however, the government celebrated a 30% drop in rainforest destruction between 2006 and 2007 - the result, they said, of an ambitious plan launched in 2004. While many argued that the drop owed more to a fall in global commodity prices, the government was euphoric. Silva, who was named as one of Brazil's 15 most influential women by Forbes magazine in 2006, hailed the news as "a great achievement for Brazilian society".

But the faultlines between Silva and other sectors of the government were becoming increasingly clear, most strikingly in relation to an economic growth plan unveiled in early 2007. Designed to help propel Brazil towards the same level of economic growth as Russia, India and China, it proposed the construction of two massive hydroelectric dams in the Amazon. Activists claim the dams, which were eventually given the green light, will displace thousands of people. Silva resisted the plans. Powerful backers of the scheme accused her of deliberately delaying environmental licences.

In January this year, the tensions grew, following the release of satellite images, produced by the government, which showed a sudden spike in deforestation. Silva called a press conference, at which she blamed the destruction in part on soy farmers clearing more land for their crops. Her comments are reported to have infuriated Lula. Silva described the rise in deforestation as a "cancer"; Lula rebutted that it was an "itch", at most a "little tumour". It was becoming obvious that something had to give. Last week, in a move widely seen as a snub to Silva, Lula placed Mangabeira Unger, known for his controversial ideas on development and industrialisation, in control of a new sustainable development scheme for the Amazon. Simultaneously, several Amazonian politicians, among them Blairo Maggi, one of the world's leading soy producers, mounted a lobby to overthrow measures that banned banks from loaning money to fund projects in areas of illegal deforestation.

"This was the last straw," says Sergio Leitao of Greenpeace. "How many times was she forced to back down? She didn't want to be responsible for this and so she said: 'Not on my watch.'"

A week on from her resignation, however, Silva is upbeat about what her ministry achieved. She talks of an environmental awakening in Brazil and around the world, "a new political pact with society that wants Brazil to develop but with the preservation of the Amazon, the Atlantic rainforest, the savannah and of all our water reserves". She is also adamant that this engagement has enabled a crackdown on the illegal loggers.

"Without the support of society it would have been impossible to have put 600 people involved in environmental crimes in the Amazon in jail," she says. "This is something that is achieved by a new social pact that is appearing inside and outside of the country."

While supporters have described her exit from power as a defeat for the green cause, she insists that progress is being made. "Twenty years ago there were politicians who promised chainsaws to their voters to win elections ... Now we have a resolution that says neither public nor private banks can fund projects in an area that is being illegally deforested."

Tomorrow, Silva will leave Brasilia and head home to Rio Branco for a short break. As she gazes down from her plane at the sprawling Amazon jungle below, she will hope and pray that, with a number of giant infrastructure projects planned in the region, history is not about to repeat itself.

"Today we are living through the challenge of prevention, of looking twice before doing something, discussing twice before doing something. Because each thing that we alter can lead to ... dramatic consequences. Those who celebrated the industrial revolution never thought that we were injuring the planet, almost fatally. We didn't have this knowledge. Today we know".