Queen Cleopatra was a descendant of Ptolemy, the Macedonian general who ruled Egypt after Alexander the Great.
But remains of the queen's sister Princess Arsinoe, found in Ephesus, Turkey, indicate that her mother had an "African" skeleton.
Experts have described the results as "a real sensation."
The discovery was made by Hilke Thuer of the Austrian Academy of Sciences.
"It is unique in the life of an archaeologist to find the tomb and the skeleton of a member of Ptolemaic dynasty," she said.
“ They were real people and not the semi-mythical figures portrayed by Richard Burton and Elizabeth Taylor ”
Archaeologist Neil Oliver
"That Arsinoe had an African mother is a real sensation which leads to a new insight on Cleopatra's family and the relationship of the sisters Cleopatra and Arsinoe."
They lived at a turbulent time when the Roman empire was extending its power across the Mediterranean.
Cleopatra established alliances with the Roman leader Julius Caesar and, after his assassination, with his political supporter, General Mark Antony, to whom she was married.
"Cleopatra, Julius Caesar, Mark Antony - they are all iconic figures from history," said archaeologist Neil Oliver who presents the BBC documentary.
"It's almost impossible to remember they were real people and not the semi-mythical figures portrayed by Richard Burton and Elizabeth Taylor. It was like a splash of cold water in the face to be confronted by them as human beings, " he continued.
"When I stood in the lab and handled the bones of Cleopatra's blood sister - knowing that in her lifetime she touched Cleopatra and perhaps Julius Caesar and Mark Antony as well - I felt the hairs go up on the back of my neck."
"Suddenly these giant figures from history were flesh and blood," said archaeologist Neil Oliver.
There was plenty of sibling rivalry between Princess Arsinoe and her powerful sister Cleopatra - many believe the queen ordered Mark Antony to murder her sister.
The film examines the life of Cleopatra - who had an affair with Julius Caesar - including her murderous intentions towards Arsinoe.
Cleopatra: Portrait of a Killer is on BBC One at 9pm on 23 March 2009.