A writer and photographer for the magazine accompanied a team of scientists to Honduras' Mosquitia region on the trail of a legendary "White City" or "City of the Monkey God."
The expedition was launched after aerial light detection scanning -- known as LIDAR
-- uncovered what appeared to be man-made structures below the rainforest, National Geographic said.
Seeking to confirm the discovery, a team of U.S. and Honduran archaeologists, a LIDAR engineer, an ethnobotanist, anthropologists and documentary filmmakers entered the remote region. They were protected by Honduran Special forces, the magazine said.
Writer Douglas Preston said the team emerged February 25, after documenting the ruins of a "vanished culture."
"In contrast to the nearby Maya, this vanished culture has been scarcely studied and it remains virtually unknown. Archaeologists don't even have a name for it," Douglas wrote. Archaeologists no longer believed in the existence of a single "White City," he said, instead believing there had been an entire civilization with many cities.
The expedition found earth works, including an earthen pyramid as well as a collection of stone sculptures, thought to potentially have been burial offerings.
Archaeologist Oscar Neil Cruz from the Honduran Institute of Anthropology and History (IHAH) estimated they dated from A.D. 1000 to 1400, Douglas wrote.
The researchers were greeted by wildlife which appeared never before to have seen humans, wandering unafraid through their camp.
"This is clearly the most undisturbed rain forest in Central America. The importance of this place can't be overestimated," ethnobotanist Mark Plotkin told National Geographic.
The team left their finds unexcavated and are keeping the exact location of the site secret in an attempt to prevent looting.
But in his article, Douglas warned that that the area was nonetheless under threat, with illegal logging for cattle farming within a dozen miles.
IHAH director Virgilio Paredes Trapero told National Geographic
that the forest and valley could disappear within eight years unless action was taken.
"The Honduran government is committed to protecting this area, but doesn't have the money. We urgently need international support."