In Latin America and the Caribbean, 89 per cent of indigenous mammals like the jaguar and anteater have been wiped out.
More than 80 per cent of freshwater populations have vanished, with freshwater fish accounting for a higher rate of extinction than any other vertebrate.
"We are the first generation to know we are destroying our planet and the last that can do anything about it," said Tanya Steele, the chief executive of the WWF. "The collapse of global wildlife populations is a warning sign that nature is dying."
Habitat loss will have a profound impact on human well-being, conservationists say.
Crops pollinated by animals account for 35 per cent of global food production, while habitat loss means that the soil for crops to grow is not being replenished with nutrients.
The loss of South American rainforests has reduced rainfall thousands of kilometres away, also imperilling crop production.
As many as 70,000 species of plants are used commercially or in medicine, posing a danger to efforts to fight disease and protect industry.