Smallpox devastated Australia’s Aboriginal communities in the late 18th century, not long after British colonists stepped foot on the continent. But historians have long debated how the disease arrived on the isolated landmass, as well as how many people it killed
Now, researchers say they’ve uncovered the answers to both questions. One new paper, which was published in 2025 as a preprint and has been accepted for publication in a peer-reviewed journal, argues that smallpox arrived on the island with the First Fleet, the 11 British ships that arrived in Sydney Harbor in January 1788 to establish a penal colony under the command of Captain Arthur Phillip. Another new paper by mostly the same researchers, also a preprint, finds that pre-colonial Australia was home to millions more Aboriginal people than earlier estimates, which suggests the death toll from the highly contagious disease was also probably much higher than previously thought.
Scientists analyzed population density estimates, mortality rates, migration pathways and other data to test the two prevailing hypotheses about how smallpox first reached Australia: with British colonists in Sydney, or with Indonesian fishermen in the northern part of the continent
Their investigation, conducted with help from computer models, ruled out the northern hypothesis. The team is convinced that smallpox arrived with the First Fleet. But how did the disease persist aboard the ships long enough to reach Australia? The fleet spent months at sea as it headed south, then east, effectively quarantining the roughly 1,500 British sailors, family members and convicts onboard, University of Tasmania historian Henry Reynolds, who was not involved with the new research, tells Science’s Andrew Curry. Additionally, records do not mention any smallpox outbreaks onboard the ships. And, even if the virus had been present, it likely would have fizzled out because of a lack of victims long before the vessels reached Australia. Individuals who contracted the disease either died within a few days or weeks, or survived and became immune.
One possibility, according to the researchers, is that the virus lived on in smallpox scabs, which doctors routinely used to inoculate patients before the first vaccine became available in 1796. They collected scabs from survivors in the end stages of the disease, crushed them into a powder and rubbed the virus-laden dust—known as variola matter—into superficial scratches on the skin
“Although ships of the British royal navy did not routinely carry variola matter, it is likely that at least one of the surgeons would have brought it along or acquired it en route in Rio de Janeiro or Cape Town,” the researchers write in the paper
Did the British colonists intentionally spread smallpox among Australia’s Aboriginal people, like they may have done with Indigenous communities in North America? The researchers note they haven’t found any formal accounts of deliberate attempts to disseminate the virus among Aboriginal groups. And they suspect that if such a plan had been undertaken, it was not at the direction of Phillip, Australia’s first governor, who “attempted to build good relationships between Indigenous groups and colonists,” they write in the paper.
However, the researchers also acknowledge that their model “cannot provide any direct evidence of the intent of the colonists during that time.”
Did you know? The history of smallpox
Smallpox has likely existed for at least 3,000 years. It was officially eradicated in 1980
In the other new paper, researchers recalculated Australia’s pre-colonial population, which earlier estimates had put between 200,000 and 800,000 individuals. Their investigation suggests the population was much higher, likely between two million and three million people
“There’s been an assumption that Aboriginal populations were quite low and their activities were ephemeral and transient,” archaeologist Alan Williams, who co-authored both papers, tells Science
The new, higher figure means British colonization likely had a much bigger effect on Australia’s Aboriginal communities than previously assumed
“We estimate that a median of 2.4 million additional people might have died through disease directly or indirectly through broader social impacts, and/or were killed in frontier violence in the early and mid-19th century,” the researchers write in the paper. “Such changes would have been catastrophic to Indigenous people, their traditional customs and life ways.”
According to the National Museum of Australia, David Collins, a British official of the Australian colony, wrote an account in April 1789 of an Aboriginal man’s reaction to the smallpox outbreak: “on taking him down to the harbor to look for his former companions, those who witnessed his expression and agony can never forget either. … Not a living person was anywhere to be met with. It seemed as if, flying from the contagion, they had left the dead to bury the dead. He lifted up his hands and eyes in silent agony for some time; at last he exclaimed, ‘All dead! All dead!’ And then hung his head in mournful silence.”
Australia’s Aboriginal population is still just a fraction of what it was before the First Fleet dropped anchor in Sydney Harbor
“It is in this context that reconciliation, engagement and future policy making must be prioritized with Indigenous people,” the researchers write
