They suggest an event that would transcend anything Biblical -- a series of blinding explosions in the atmosphere equivalent to thousands of atomic bombs, the researchers said.
The so-called nanodiamonds are made under high-temperature, high-pressure conditions created by cosmic impacts, similar to an explosion over Tunguska in Siberia that flattened trees for miles in 1908.
Doug Kennett of the University of Oregon and colleagues found the little diamonds at sites from Arizona to South Carolina and into Alberta and Manitoba in Canada.
They are buried at a level that corresponds to the beginning 12,900 years ago of the Younger Dryas, a 1,300-year-long cold spell during which North American mammoths, saber-toothed cats, camels and giant sloths became extinct.
The Clovis culture of American Indians also appears to have fallen apart during this time.
Bones of these animals, and Clovis artifacts, are abundant before this time. Excavations show a dark "mat" of carbon-rich material separates the bones and artifacts from emptier and younger layers.
Writing in the journal Science, Kennett and colleagues report they have evidence of the nanodiamonds from six sites across North America, fitting in with the hypothesis that a giant explosion, or multiple explosions, above the Earth's surface cause widespread fire and pressure.
There is evidence these minerals can be found in other sediments, too, they said, and help explain the "black mat".
"These data support the hypothesis that a swarm of comets or carbonaceous chondrites (a type of meteorite) produced multiple air shocks and possible surface impacts at 12,900 (years ago)" they wrote.
The heat and pressure could have melted part of the Greenland ice sheet, causing currents to change and affecting climate. Any impacts would have kicked up dust that would have shrouded the sun and lowered temperatures, endangering plants and animals.
"The nanodiamonds that we found at all six locations exist only in sediments associated with the Younger Dryas Boundary layers, not above it or below it," Kennett, an archeologist, said in a statement.
"These discoveries provide strong evidence for a cosmic impact event at approximately 12,900 years ago that would have had enormous environmental consequences for plants, animals and humans across North America."
(Reporting by Maggie Fox, editing by Philip Barbara)