The lineage found, named C1e, is also mitochondrial, which means that the genes were introduced into Iceland by a woman.
"As the island was virtually isolated from the 10th century, the most likely hypothesis is that these genes corresponded to an Amerindian woman who was brought from America by the Vikings around the year 1000," said Lalueza-Fox.
The researchers used data from the Rejkjavik-based genomics company deCODE Genetics.
He said the research team hopes to find more instances of the same Native American DNA in Iceland's population, starting in the same region in the south of the country near the massive Vatnajokull glacier.
The report, by scientists from the CSIC and the University of Iceland, was also published in the latest edition of the American Journal of Physical Anthropology.
The journal said 75 to 80 percent of contemporary Icelanders can trace their lineage to Scandinavia and the rest to Scotland and Ireland.
But the C1e lineage is "one of a handful that was involved in the settlement of the Americas around 14,000 years ago.