For centuries, historians have debated what caused the Plague of Justinian, the world’s first recorded pandemic.
Now, for the first time, scientists have found direct genetic proof that the bacterium Yersinia pestis—the same microbe that causes plague today—was behind the devastating outbreak nearly 1,500 years ago.
An international team led by the University of South Florida and Florida Atlantic University, with collaborators in India and Australia, made the breakthrough at the ancient city of Jerash in Jordan, close to where the pandemic was first described in the year 541.
Excavations at a mass grave beneath the city’s former Roman hippodrome revealed human teeth carrying DNA from Y. pestis.
“This discovery provides the long-sought definitive proof of Y. pestis at the epicenter of the Plague of Justinian,” said Rays H. Y. Jiang of USF. “For centuries, we’ve relied on written accounts of a devastating disease, but lacked biological evidence. Our findings finally provide that missing piece.”
The Plague of Justinian raged between CE 541 and 750, killing tens of millions of people, reshaping the Byzantine Empire, and changing the course of Western civilization.
Until now, traces of plague had only been recovered thousands of miles away in small European villages, leaving doubts about what struck the heart of the empire.
By sequencing DNA from eight teeth found in Jerash, researchers confirmed that victims carried nearly identical strains of Y. pestis.
That genetic similarity points to a rapid, overwhelming outbreak, matching historical records of a plague that struck suddenly and wiped out entire communities. The fact that Jerash’s grand hippodrome, once a hub of entertainment, became a mass grave shows how unprepared cities were for the scale of the disaster.
A companion study placed the Jerash evidence in a wider evolutionary context, comparing hundreds of ancient and modern Y. pestis genomes.
The analysis showed that plague has been circulating among humans for millennia and that later pandemics, such as the Black Death of the 14th century, did not descend from one ancestral strain but instead erupted independently from long-lasting animal reservoirs.
This explains why plague has reappeared in multiple waves across different times and regions, unlike modern pandemics such as COVID-19, which stemmed from a single spillover event.
The discovery is not just about the past. Plague still exists today, although rare. In July, a resident of Arizona died from pneumonic plague, the first such case in the U.S. in nearly two decades, and another case was confirmed in California last week.
“We’ve been wrestling with plague for thousands of years and people still die from it today,” said Jiang. “Like COVID, it continues to evolve, and containment measures can’t eliminate it completely.”
The team is now expanding their work to Venice, where mass graves from the Black Death may provide further insights into how societies fought to contain pandemics.
By combining archaeology and genomics, researchers hope to better understand how pandemics emerge, recur, and shape human history.
