Polar bears and penguins are among the species under greatest threat.
Current projections suggest that by 2100 Marine Protected Areas (MPAs) will be 2.8 degrees Celsius warmer than today – enough to make them uninhabitable for many of the fish, mammals, birds and invertebrates, according to the researchers.
There are 8,236 MPAs around the world, covering 4% of the total surface of the ocean.
They were set up to provide safe havens for wildlife and conserve endangered habitats by restricting human activities such as fishing, mining and tourism.
The new study, published in the journal Nature Climate Change, suggests that without drastic action MPAs will be “devastated” by rapid global warming.
Lead scientist Professor John Bruno, from the University of North Carolina in the US, said: “With warming of this magnitude, we expect to lose many, if not most, animal species from MPAs by the turn of the century.
“To avoid the worst outcomes, we need to immediately adopt an emission reduction scenario in which emissions peak within the next two decades and then decrease very significantly, replacing fossil fuels with cleaner energy sources like solar and wind.”
The scientists carried out simulations to model sea surface temperatures and oxygen concentrations in MPAs around the world, including those where fishing is banned.
They found that even under the Intergovernmental Panel on Climate Change (IPCC) “business-as-usual” emissions scenario, MPAs were expected to warm by 0.034 degrees Celsius per year, resulting in an average increase of 2.8C by the end of the century.
For each MPA the scientists calculated a “community thermal safety margin” (CTSM), the critical point after which most species would not be able to tolerate further temperature change.
In tropical areas, this threshold was expected to be reached by about 2050.
MPAs in the Arctic and Antarctic are considered to be among those areas at greatest risk, said the scientists.