Analysis of a bone discovered in a Siberian cave revealed the female, who died 90,000 years ago, had a Neanderthal mother and a Denisovan father.
The 13-year-old girl, nicknamed "Denny" by scientists, is an example of interbreeding between now-extinct human groups, say scientists.
Denisovans, now extinct, were a group of humans first identified from DNA analysis of a finger bone discovered in the Denisova cave in the Altai Mountains of Russia a decade ago.
Neanderthals, also now extinct, also lived in the cave.
Pontus Skoglund, population geneticist at the Francis Crick Institute in London, said: "To find a first-generation person of mixed ancestry from these groups is absolutely extraordinary.
"It's really great science coupled with a little bit of luck."
The complete picture of Denny's ancestry had been incomplete for a number of years - only her mother's side was known after researchers discovered mitochondiral DNA in her remains came from a Neanderthal.
The most recent study set out to compare DNA variation in Denny with that of three other hominins, a Neanderthal, a Denisovan and a modern-day human (Homo Sapien) from Africa.
Palaeogeneticists Viviane Slon and Svante Paabo at Germany's Max Planck Institute for Evolutionary Anthropology carried out genome analysis on a bone taken from the Denisova cave in Russia.
A 40 per cent match was found with the Denisovan, as well as a 40 per cent match for the Neanderthal, while bone density gave away the teenager's age.
Scientists confirmed Denny came from two separate hominins - and not two hybrids - by looking at where the genomes between Neanderthals and Denisovans differ.
After comparing Denny's DNA to genomes of a Neanderthal and a Denisovan, researchers found she had one set of chromosomes from each hominin.
Scientists have been aware of breeding between different human groups, including between Denisovans and Homo Sapiens, thanks to variation among humans.
But this is the first time a first-generation offspring from the pairing has been discovered.
Scientists now think such a mix could be more common than initially thought.
"We knew from previous studies that Neandertals and Denisovans must have occasionally had children together, but I never thought we would be so lucky as to find an actual offspring of the two groups," said Slon.
The findings were published in Nature.
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