New modeling reveals up to 220,000 Indigenous Australians died in 1789 smallpox epidemic

In 1789, shortly after British ships dropped anchor in Sydney Harbour, smallpox began moving through First Nations communities with terrifying speed. A new mathematical model published this week in Nature Human Behaviour suggests the death toll was staggering: somewhere between 40,000 and 220,000 Indigenous Australians perished in that initial outbreak. For more than two centuries, historians debated where the disease came from. Now researchers have an answer.

The work emerged from the ARC Centre of Excellence for Indigenous and Environmental Histories and Futures, based at James Cook University in Cairns, conducted in close partnership with the Gujaga Foundation representing the Dharawal Nation—the people who stood at the epicenter when the epidemic struck. The team, led by Distinguished Professor Sean Ulm, used computational modeling to test competing theories about the outbreak's origin. Did it arrive with Makassan traders visiting the north? Or did it come with the First Fleet to Sydney? The researchers built models that accounted for how people actually moved across the continent before colonization: along known paths to water sources, ceremonial sites, food grounds, and family connections. They then asked whether smallpox could have traveled from the north to Sydney under realistic movement patterns. The answer was unambiguous. "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," Dr. Cody Nitschke, the study's lead author, explained. The disease originated in Sydney Harbour with the First Fleet.

What made this epidemic so catastrophic was not just its speed but its concentration. The virus followed coastlines and major river systems—the Murray, the Lachlan—but did not sweep across the entire continent. It ravaged south-eastern Australia with particular ferocity. Smallpox kills through fever and severe illness, leaving survivors scarred if they survive at all. For populations with no prior exposure, the death rate climbs sharply. The modeling suggests a lethality rate around 60 percent in the affected regions, though the true figure remains uncertain. What is certain is the scale of loss: entire family groups vanished. Elders, children, and pregnant women were especially vulnerable, which meant that knowledge, language, and cultural practice suffered alongside the bodies themselves.

David Ingrey, a senior Elder in the La Perouse Community of the Dharawal Nation, spoke to what this research confirms for his people. "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," he said. "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." The finding resolves a historical question that had divided scholars for decades, but it also carries weight beyond academic debate. It names the source of a catastrophe that reshaped the continent.

Yet the story does not end in 1789 or in the years immediately after. Professor Corey Bradshaw, a chief investigator on the project, noted that the epidemic's effects ripple forward to the present day. Families were fractured. Knowledge systems were damaged. Ways of caring for Country—the land itself, understood as a living entity requiring relationship and responsibility—were disrupted. Survivors were often too weakened to maintain the practices that held culture together. The disease did not merely kill individuals; it severed connections between generations.

But the Dharawal people did not disappear. Shane Ingrey of the Gujaga Foundation emphasized a fact often obscured by the scale of the catastrophe: "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." Within weeks, survivors had regrouped. Over the following century, they continued to live in and around the harbour, speaking their language, practicing their knowledge systems, maintaining their culture. When the Australian government forcibly relocated the remaining Dharawal descendants to La Perouse in the 1880s, they carried that continuity with them. "Our connections were disrupted, but they were never broken," Ingrey said.

The researchers acknowledge that this modeling addresses only the first outbreak. Later epidemics and frontier violence—the systematic killing and displacement that followed colonization—remain to be fully understood and quantified. Professor Lynette Russell noted that the findings have been welcomed by international colleagues, including researchers in Makassar who have long rejected the theory that their ancestors brought the disease south. The work stands as a collaboration between Indigenous scholars and academic institutions, a deliberate effort to ground historical understanding in both data and the knowledge held by the communities who lived through it. As Professor Bradshaw emphasized, "The modelling does not speak over Aboriginal knowledge, memory, or oral history." The numbers tell part of the story. The rest belongs to those who survived and to those who carry the memory forward.