The research throws up a new riddle in the story of human evolution, since it shows that the ancient Spaniard was related to a mysterious group of early humans from Siberia.
The DNA belonged to a type of human that long pre-dated our own, whose fossils have been found in large numbers at La Sima de los Huesos - the "bone pit" - at Atapuerca, northern Spain.
Although the species has been classified as Homo heidelbergensis, it also bears traits typical of Neanderthals. Scientists were able to sequence almost the complete genetic code, or genome, from the creature's mitochondria, tiny power houses in cells that generate energy. Mitochondrial DNA is only passed down from mothers and can be used to track lineages.
The study revealed a surprise. Instead of the expected link with the Neanderthals, researchers found genetic similarities with the Denisovans, an enigmatic eastern Eurasian group from Siberia that lived far from Spain. Around 40,000 years ago, Denisovans co-existed alongside Neanderthals and early modern humans, and they may have interbred.
Professor Svante Paabo, director of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, said: "This opens prospects to study the genes of the ancestors of Neanderthals and Denisovans. It is tremendously exciting."