No trace of the lineage appears to remain today, meaning that the "ice man" - dubbed "Oetzi" - is unlikely to have any descendants.
Oetzi's mummified remains were found in September 1991 in the Eastern Alps near the Austro-Italian border.
He was about 46 years old when he met his violent death. Examinations revealed that he had been wounded by an arrow and possibly finished off with a mace blow to the face.
Since 1998 he has been on display at the South Tyrol Museum of Archaeology in Bolzano, Italy.
Scientists have now built up a complete picture of Oetzi's mitochondrial DNA, which is always passed down to future generations by mothers. This is DNA in the mitochondria, tiny power plants in cells that generate energy.
The team had a surprise when they tried to determine which genetic branch of the human family tree Oetzi belonged to.
Although he fell into a subgroup called K1, his lineage did not match any of the three known K1 "clusters".
Professor Martin Richards, from the University of Leeds, said:
"Our analysis confirms that Oetzi belonged to a previously unidentified lineage of K1 that has not been seen to date in modern European populations.
"The frequency of genetic lineages tends to change over time, due to random variations in the number of children people have - a process known as 'genetic drift' - and as a result, some variants die out.
"Our research suggests that Oetzi's lineage may indeed have become extinct."
The findings appear in the journal Current Biology.
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