Researchers warn climate change could reduce life in the oceans' "twilight zone", which is 200 to 1,000 metres deep, by 20-40 per cent by the end of the century.
They also said that in a future of high-emissions, life in the twilight zone, stands to be severely depleted within 150 years, with no recovery for thousands of years.
Twilight zone in oceans gets little light but is home to a wide variety of organisms and billions of tonnes of organic matter.
The researchers from universities in the UK have described their findings in the journal Nature Communications.
The researchers said that while relatively little is known about the ocean twilight zone, what may happen in the future could be understood from past experience.
The team, made up of palaeontologists and ocean modellers, looked at records from preserved microscopic shells in ocean sediments and studied the abundance of life in the twilight zone in past warm climates.
"We looked at two warm periods in the Earth's past, about 50 million years ago and 15 million years ago," said Professor Paul Pearson of Cardiff University, who led the research.
"In these warm periods, far fewer organisms lived in the twilight zone, because much less food arrived from surface waters," said Pearson.
The study showed that in warmer seas of the past, organic matter sunk down from the ocean surface and fed upon by animals in the twilight zone was degraded much faster by bacteria - meaning less food reached the twilight zone.
"The rich variety of twilight zone life evolved in the last few million years, when ocean waters had cooled enough to act rather like a fridge, preserving the food for longer, and improving conditions allowing life to thrive," said Katherine Crichton, from the University of Exeter, and lead author of the study.
To understand what would happen in future decades, centuries and millennia, they combined evidence on past warm periods with Earth System Model simulations.
"Unless we rapidly reduce greenhouse gas emissions, this could lead to the disappearance or extinction of much twilight zone life within 150 years, with effects spanning millennia thereafter.
The study's three emissions scenarios are based on total carbon dioxide emissions after 2010. "Low" is 625 billion tonnes, "medium" is 2,500 billion tonnes, and "high" is 5,000 billion tonnes.
Emissions have been close to 40 billion tonnes every year from 2010-22, so most of the carbon dioxide, about 500 billion tonnes, for the study's "low" scenario has already been emitted.
At the current rate, the researchers said that the "medium" scenario would be reached 50 years from now, and the "high" in just over a century.
"The twilight zone plays an important role in the ocean's carbon cycle because most of the carbon dioxide taken up by phytoplankton ends up there as their remains sink down from the surface ocean," said Jamie Wilson, from the University of Liverpool.