Groundbreaking modelling has revealed that as many as 220,000 Indigenous Australians may have died in a devastating 1789 smallpox outbreak that originated in Sydney, tracing its origins directly to the First Fleet.

Soon after British ships arrived, smallpox swept through First Nations communities in the Sydney area, and many died as a result. The study found that the epidemic had a devastating demographic impact and lasting ramifications for how First Nations people resisted colonisation and their capacity to manage Country, with effects still felt today.

“Our modelling shows a rapid smallpox spread and mass mortality after colonial exposure,” said Dr Cody Nitschke, Research Associate in the ARC Centre of Excellence for Indigenous and Environmental Histories and Futures at Flinders University. “It’s important for Australians to come to terms with this traumatic legacy.”

Published in the journal Nature Human Behaviour in collaboration with the Gujaga Foundation of the Dharawal Nation, whose ancestors were at ground zero, the findings provide important insights into the outbreak — including how quickly it spread through Aboriginal communities in south-eastern Australia. The disease caused fever, severe illness, scarring and high death rates, especially in Indigenous populations with no previous exposure, and it followed coastlines and major rivers. Importantly, the first epidemic did not spread Australia-wide.

Tracing the Epidemic’s True Origin

“The epidemic was likely limited to the south-eastern coastal regions of Australia and along major intersecting rivers such as the Murray and Lachlan Rivers. Assuming a 60% lethality, the loss of between 40,000–220,000 people would probably have occurred in these regions,” said Dr Nitschke.

The researchers, including Indigenous scholars, tested whether the epidemic originated from Makassan visitors to northern Australia from island Southeast Asia, or from Europeans on the First Fleet. “Rather than relying on assumptions about where the epidemic started, we tested the two main origin stories directly. The data allowed us to weigh those explanations against each other and identify which one was most consistent with how the disease spreads,” Dr Nitschke said.

“Before colonial invasion, the movement of people followed known paths — for water, ceremony, food, trade, and family. The disease could only travel where people could realistically walk, rest, and recover. Even after adding generous movement rates and idealised contact between populations, the model showed that smallpox was extremely unlikely to have reached Sydney if introduced in the north.”

Professor Corey Bradshaw, co-author and Chief Investigator in the ARC Centre of Excellence for Indigenous and Environmental Histories and Futures at Flinders University, said the evidence outlines the catastrophic impact of smallpox on Indigenous communities, including enduring intergenerational effects.

“The smallpox epidemic is arguably one of the most devastating events resulting from colonial invasion, yet there remains widespread disagreement on its origin, scale, impact, and spread until this modelling gave us important new insights. Families, knowledge systems, and ways of caring for Country were badly damaged, and the effects are still felt today,” Professor Bradshaw said.

“This devastating epidemic was concentrated and likely unfolded over many years. Elders, children, and pregnant women were especially vulnerable, meaning that knowledge, language, and culture suffered deep harm alongside population loss. Even survivors were severely compromised, and could often not care for Country in the same way as before the infection.”

Honoring Community Knowledge and Survival

Although the modelling shows it is unlikely that other parts of Australia were affected by the initial epidemic, the researchers recommend revisiting assumptions about the subsequent impact of other diseases and frontier violence on Indigenous communities. “The modelling does not speak over Aboriginal knowledge, memory, or oral history,” Professor Bradshaw said.

“We always believed that it was the First Fleet that spread the smallpox, with many families within community suspecting it was spread deliberately too but this still needs to be looked at. This paper shows that it didn’t come from up north. We know it didn’t start with the French visitors. It was started in Sydney Harbour with the First Fleet,” said David Ingrey, a senior Elder in the La Perouse Community of the Dharawal Nation.

Dr Shane Ingrey of the Gujaga Foundation and a Research Associate in the ARC Centre of Excellence for Indigenous and Environmental Histories and Futures at the University of New South Wales added: “It is always perceived by the wider community that everyone was wiped out and there were no Sydney Aboriginal people left after the initial outbreak, but we have First Fleet observations of our people back in the harbour within a month or so fishing and living.”

“We quickly regrouped and over the next century continued living in and around the Harbour, continuing our cultural ways, continuing talking our language, continuing to apply our knowledge systems right up until the 1880s where the remaining descendants were forcibly relocated on Country out to the old camp turned government reserve at La Perouse. Here we continued to practice and pass on our Dharawal culture and language and still do today. Our connections were disrupted but never broken.”

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Journal: Nature Human Behaviour
Article Title: Stochastic models indicate rapid smallpox spread and mass mortality of Indigenous Australians after colonial exposure
DOI: 10.1038/s41562-026-02504-6
Funding: Australian Research Council Centre of Excellence for Indigenous and Environmental Histories and Futures; Australian Research Council Laureate Fellowship; Australian Research Council Discovery Early Career Researcher Award; Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage