The discovery by UK researchers was made almost a km below the surface in an undersea crater near the South Sandwich Islands.
Worldwide, only six natural whale skeletons have ever been found on the seafloor. Scientists have previously studied whale carcasses, known as a 'whale fall', by sinking bones and whole carcasses. Despite large populations of whales in the Antarctic, whale falls have not been studied in this region until now.
"The planet's largest animals are also a part of the ecology of the very deep ocean, providing a rich habitat of food and shelter for deep sea animals for many years after their death," said Diva Amon, lead author of the paper based at University of Southampton Ocean and Earth Science (which is based at NOC) and the Natural History Museum.
"At the moment, the only way to find a whale fall is to navigate right over one with an underwater vehicle," said co-author Dr Jon Copley of University of Southampton Ocean and Earth Science.
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"We were just finishing a dive with the UK's remotely operated vehicle, Isis, when we glimpsed a row of pale-coloured blocks in the distance, which turned out to be whale vertebrae on the seabed," said Copley.
Bacteria break down the fats stored in whale bones, for example, and in turn provide food for other marine life. Other animals commonly known as zombie worms can also digest whale bone.
Researchers believe the skeleton may have been on the seafloor for several decades.
Samples also revealed several new species of deep-sea creatures thriving on the whale's remains, including a 'bone-eating zombie worm' known as Osedax burrowing into the bones and a new species of isopod crustacean, similar to woodlice, crawling over the skeleton.
The study is published in Deep-Sea Research II: Topical Studies in Oceanography.