Neanderthals had a long history of inbreeding and incest was commonplace across their communities, researchers have said.
Experts from the University of California, Berkeley, say the DNA sequence from a Neanderthal female toe shows her mother and father were potentially brother and sister.
Scientists undertook the most complete DNA sequence to date from the 50,000-year-old toe bone to find out the genetic history of its owner.
The woman's genome indicated that she was the daughter of a very closely related mother and father, who could have been half-siblings with the same mother.
The woman's parents could also have been uncle and niece, aunt and nephew, grandparent and grandchild or double first cousins, which involves the offspring of two siblings who married siblings.
Further examination of the bone suggested the population size of Neanderthals at the time was very small and that inbreeding was more common in Neanderthal groups than in modern populations or in Denisovan, another branch of early human.
One of the researchers, Fernando Racimo, identified 87 specific genes in modern humans that are significantly different from related genes in Neanderthals and Denisovans, which they say may hold clues to behavioural differences and why these early humans died out.
"There is no gene we can point to and say 'this accounts for language or some other unique feature of modern humans'," fellow researcher Montgomery Slatkin said.
"But from this list of genes, we will learn something about the changes that occurred on the human lineage, though those changes will probably be very subtle."
The experts also found there was massive interbreeding among early human species thousands of years ago. Findings show that Denisovans bred with a mystery fourth group of early humans who lived in Eurasia at the same time.
"The paper really shows that the history of humans and hominins during this period was very complicated," said Slatkin, a UC Berkeley professor of integrative biology.
"There was lot of interbreeding that we know about and probably other interbreeding we haven't yet discovered."