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By then, twice as many mammals as now will be at risk of extinction, say conservationists.
Climate change, loss of rainforest and hunting is a threat to many rare mammals on the island.
But there is hope for species like the orang-utan if action is taken to focus conservation efforts on upland areas, scientists report in Current Biology.
Borneo is the world's third largest island, accounting for 1% of the world's land yet about 6% of global biodiversity.
The island has already lost over half its forests, a third disappearing in the last three decades.
A team led by researchers at the Durrell Institute of Conservation and Ecology, University of Kent, UK,  used modelling and satellite images to predict where rainforest will be lost over the next 65 years, based on predictions of climate change and changes in land use.
Working with institutes in Germany, Australia and Indonesia, they mapped the likely suitable habitat for each of 81 Bornean mammals.
They found that deforestation and climate change would lead to 30-49% of mammals losing at least a third of their habitat by 2080.
This would put at least 15 carnivores, 8 primates and 21 bat species at risk of extinction by 2080, almost doubling the proportion of threatened mammals on the island, according to the research.
But there is hope that better forestry management for conservation outside existing reserves could curb this loss, said lead researcher Dr Matthew Struebig.
"Only a modest amount of additional land on Borneo (~28,000 km2, or 4% of the island) would be needed to safeguard many mammal species against threats from deforestation and climate change."
The logging industry had a major role to play in conservation, given that they manage much of the land, he added.
And since deforestation and climate change is likely to have the biggest impact on lowland forests, it made sense to target efforts to forests at higher elevations.
Special efforts are needed for species like the flying fox and otter civit that would be unable to adapt to higher altitudes, said Dr Struebig.
"It is not so much that species would be doomed, but more that their area requirements would unlikely be met in the land available for conservation," he explained.
Writing in the journal Current Biology, the researchers described the outlook as "pessimistic", but said improving conservation outside existing reserves could help meet biodiversity goals.
Half of Borneo's mammals will see their habitats shrink by at least a third by 2080, according to a study.