The two co-existed before the European Hunter-gatherer communities died out or were absorbed into the farming population around 5,000 years ago, researchers said.
Researchers describe their analysis of DNA and isotopes from human bones found in the 'Blatterhohle' cave near Hagen in Germany, where both hunter-gatherers and farmers were buried.
The team, led by anthropologist Professor Joachim Burger of the Johannes Gutenberg University, Germany, used stable isotopes to determine their diet, DNA to investigate how they were related, and radiocarbon to establish how old the bones were.
"It is commonly assumed that the European hunter-gatherers disappeared soon after the arrival of farmers," said Dr Ruth Bollongino, lead author of the study.
"But our study shows that the descendants of the first European humans maintained their hunter-gatherer way of life, and lived in parallel with the immigrant farmers, for at least 2,000 years. The hunter-gathering way of life only died out in Central Europe around 5,000 years ago, much later than previously thought," said Bollongino.
"Until around 7,500 years ago all central Europeans were hunter-gatherers," said Professor Mark Thomas, professor of evolutionary genetics at UCL, and a co-author of the study.
"They were the descendants of the first wave of our species to arrive in Europe, around 45,000 years ago. They survived the last Ice Age and the warming that started around 10,000 years ago. And now it seems they also survived the initial wave of farmers spreading across Europe from the southeast of the continent," said Thomas.
Previous genetic studies by Burger and Thomas showed that agriculture was brought to Central Europe by immigrant farmers around 7,500 years ago.
From that time on, little trace of hunter-gathering can be seen in the archaeological record, and it was widely assumed that the hunter-gatherers rapidly died out or were absorbed into the farming populations.
"However, our study now shows that the hunter-gatherers stayed in close proximity to farmers, had contact with them for thousands of years, and buried their dead in the same cave," said Burger.
"This contact was not without consequences, because hunter-gatherer women sometimes married into the farming communities, while no genetic lines of farmer women have been found in hunter-gatherers," he said.
The study was published in the journal Science.


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