Among the nine affected trees were four of Africa's largest baobabs.
Overall, five of the six largest baobabs either died or their oldest parts significantly deteriorated.
None of the trees showed obvious signs of infection, the researchers found, and the pattern of deaths did not fit what would be expected had the die-off been caused by a contagious disease. Over 15 years, Patrut identified about 60 of the largest and oldest baobabs. The work also addresses the mystery of why so many of these odd trees are dying.
The researchers set out to date the trees, but discovered that they were dying in an "event of unprecedented magnitude", they write.
Also known as "dead-rat" trees, after the shape of their fruit, baobab trees have stout, branchless trunks.
Scientists have been monitoring the baobab trees across southern Africa since 2005.
Despite typical lifespans of hundreds or even thousands of years, Africa's baobab trees are dying off rapidly, according to a new study by ecologists.
The new research, by Adrian Patrut of Babes-Bolyai University in Romania and an global group of colleagues, finds that in the past 12 years, "9 of the 13 oldest and 5 of the 6 largest individuals have died, or at least their oldest parts/stems have collapsed and died". So the scientists instead used accelerator mass spectrometry to perform radiocarbon dating on samples from the largest, oldest trees in southern Africa.
Study leader Adrian Patrut‚ from Babes-Bolyai University in Romania‚ said: "It is definitely shocking and dramatic to experience during our lifetime the demise of so many trees with millennial ages".
Beginning in Spring 2016, the tree began to split apart.
The others saw the death of one or several parts. But in 2011 the oldest known specimen-a shrine for rainmakers named Panke that sprouted about 2450 years ago-died and toppled over.
The latest survey of ancient baobabs suggests climate change may already be affecting the continent's vegetation.
"We suspect this is associated with increased temperature and drought", Dr Patrut told BBC News. The common theory, Baum said, is that as the tree slowly grows around these scars, they can become large hollows. Dry conditions and increasing temperatures might have something to do with the sudden deaths, but the scientists say that more research is needed to know for sure.
Whatever the cause, these mysterious deaths will have a big impact on the southern African landscape. Again, it's hard to determine exactly what caused their demise, but the researchers strongly suspect the deaths are associated at least partly "with significant modifications of climate conditions that affect southern Africa in particular".
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