Mineral deposits and cool conditions kept Cheddar Man's DNA intact enough for researchers to sequence many of its fragments.
The Natural History Museum and University College London collaborated on the recent research.
Cheddar Man would have lived a hunter-gatherer lifestyle, making sharp blades from flints for butchering animals, using antlers to whittle harpoons for spear fishing and carving bows and arrows.
But an unprecedented examination of his DNA, along with a facial reconstruction of the fossil, shows that the young man would have had a darker complexion than previously thought, along with blue eyes and dark, curly hair.
This shows similarities with the findings of Cheddar Man who has DNA linking him to migration from Spain, Hungary and Luxembourg sometime after the last Ice Age.
The research points to a Middle Eastern origin for Cheddar Man, suggesting that his ancestors would have left Africa and then moved into the Middle East.
Around 10 percent of the British population shares DNA with the Mesolithic population to which the Cheddar Man belonged, but they aren't direct descendents.
Model makers, Adrie and Alfons Kennis, used a hi-tech scanner to render Cheddar Man's skull in full three-dimensional detail, fleshing it out with facial features based on the results of the scientific research. The Kennis brothers are experts in recreating scientifically accurate animals and humans, with a focus on human evolution. It's always been understood that our earliest ancestors were black and that the lighter skin pigmentation present across northern Europe evolved relatively recently in human history.
Cheddar Man - who had previously been portrayed as having brown eyes and light skin - was among the first permanent settlers to make the United Kingdom their home, and is related to around 10 percent of the modern population there.
National identity in modern Britain is complicated to say the least.
Perhaps what's most remarkable about this Cheddar Man news is a hard truth.
The team homed in on genes known to be linked to skin color, hair color and texture, and eye color.
This allowed the team to compare markers for physical traits, and determine what the Cheddar Man could have looked like. He adds: "We're delighted to be playing a part in these historic findings".
Britain's oldest complete skeleton, known as Cheddar Man, was unearthed more than a century ago in Gough's Cave in Somerset.
To extract the DNA, researchers and scientists working on the project, had to insert a small incision into the skull by drilling into the bone.
The analysis also ruled out an ancestral link with individuals inhabiting Gough's Cave 5,000 years earlier, who appear to have performed grisly cannibalistic rituals, including gnawing on human toes and fingers - possibly after boiling them - and drinking from polished skull cups. Humans had lived in Britain off and on for thousands of years before his time, but they had been wiped out during periodic ice ages. "As these continue to develop, we will be able to learn even more".