The source of the 1789 smallpox outbreak that devastated the Indigenous population in Australia has been widely debated. Now, a new modeling study uses mathematical modeling, historical records, archaeology, and demographic data to show the disease’s far-reaching impact on Indigenous Australians. The study rejects the long-standing theory that the disease spread southward from Indonesian (Makassan) traders, and argues that the British First Fleet sent to settle Australia brought smallpox to the continent near Sydney Cove soon after British settlement in 1788.
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Outbreak Source Was Vials of Dried Smallpox Scabs
Alan Williams, an archaeologist at the private firm EMM Consulting and co-author of the study, “Stochastic models indicate rapid smallpox spread and mass mortality of Indigenous Australians after colonial exposure,” published July 9th in the journal Nature Human Behaviour, argues that the likely source of the outbreak was vials of dried smallpox scabs that British medics had kept for inoculations. This medical practice was a precursor to smallpox vaccines, invented by Edward Jenner in the 1790s. Previously, historians had maintained that the live smallpox virus could not have survived an 8-month journey from Portsmouth, England, to Botany Bay, south of modern-day Sydney, Australia. However, according to Williams, the vials of smallpox scabs may have been replenished during the voyage when the fleet stopped at either Cape Town, South Africa, or Rio de Janeiro, Brazil, only a few months earlier.
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An historical engraving depicting one of the earliest encounters between Aboriginal Australians and members of the British First Fleet following the establishment of the colony at Sydney Cove in 1788. These first contacts occurred shortly before the devastating 1789 smallpox epidemic that transformed Indigenous communities. (Andrew Garran/Public domain)
The First Fleet Took Possession of the Continent
The British “First Fleet” to Australia consisted of 11 ships: two naval vessels, six convict transports, and three ships for provisions. The British claimed that, legally, Australia lacked any authority and belonged to no one. Soon after dropping anchor off Botany Bay, the Royal Navy determined that they needed to depart because the land was quite poor and water supplies were insufficient. Consequently, they soon raised anchor and relocated to Sydney Cove in Port Jackson, now part of modern-day Sydney.
Officers raised the British flag at this new location, claiming the entire continent for King and Country. At this point, there were no signs of a smallpox outbreak among nearby native Australian communities, but evidence of the devastating toll emerged in the subsequent decades. Unfortunately, there were no official records of smallpox cases among the native population, only oral histories, journals, or first-person accounts of the disease.
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Captain Watkin Tench (1758–1833), British Marine officer and First Fleet chronicler. His journals provide some of the earliest eyewitness accounts of the devastating 1789 smallpox epidemic among Indigenous Australians and remain essential primary sources for historians studying the outbreak. (Frederick Buck/Public Domain)
Smallpox Decimated the Indigenous Communities
The smallpox outbreak decimated the Indigenous communities and contributed to the rapid demise of native Australian culture. The study estimated that approximately 220,000 people died from the disease, and that early-20th-century Australian authorities didn’t have an accurate estimate of the Indigenous population when they initially documented historical accounts of the smallpox outbreak.
The new computer modeling traced the spread of the disease, demonstrating that the outbreak could not have spread southward from Indonesian traders. Williams notes, “Among other principal issues, the two regions were separated by thousands of miles of uninhabited desert.”
Further, modeling of the smallpox outbreak in native communities near Port Jackson indicated that the disease outbreak had started from this particular point. Co-author Matthew Cody Nitschke, an expert in computer modeling at Flinders University in Adelaide, maintains that “there is very strong evidence that it was the First Fleet.” At that point in time, disease transmission wasn’t well understood; therefore, the spread of smallpox may have happened by pure accident. The research focuses on identifying the probable origin of the outbreak rather than attributing intentional responsibility.
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David Collins was a Royal Marine officer, Judge Advocate of the First Fleet, and one of the earliest historians of colonial Australia. Collins accompanied Governor Arthur Phillip aboard the First Fleet in 1787 and remained in New South Wales during the colony's formative years. His two-volume work, An Account of the English Colony in New South Wales (1798–1802), remains one of the principal primary sources describing the establishment of the colony and the devastating 1789 smallpox epidemic among Indigenous Australians. (Unknown Author/Public Domain)
A Second Study Report Corrects Historical Population Data
The study authors are preparing a second report providing evidence that there were between three and five million native Australians when the British First Fleet anchored off Australia - far more than the 300,000 Indigenous Australians estimated in earlier studies, especially in the resource-rich areas making up the North and Southeast of the continent. The former estimate of roughly 300,000 Indigenous Australians is ascribed to a 1930s study, based only on their depleted numbers. Williams explains: “By the time people actually sat down and said how many people were here, we had 100 years of disease, frontier violence, and everything else going on.”
Ann McGrath, a historian at the Australian National University in Canberra who wasn’t involved in the study, was impressed by the methods researchers applied: “The strong interdisciplinary approach of this latest research convincingly refutes this, and it also provides a much expanded estimate of the Indigenous population before 1788.”
Top Image: Arthur Phillip, commander of the First Fleet and first Governor of New South Wales. Phillip's journals recorded the devastating 1789 smallpox epidemic among Indigenous Australians shortly after the establishment of the British colony at Sydney Cove. Source: Francis Wheatley/Public Domain
By Ramsey Hardin
References
Collins, David. An Account of the English Colony in New South Wales. London: T. Cadell Jr.
and W. Davies, 1798. https://gutenberg.net.au/ebooks/e00011.html
Dowling, Peter. Fatal Contact: How Epidemics Nearly Wiped Out Australia's First Peoples.
Clayton, VIC: Monash University Publishing, 2021.
https://publishing.monash.edu/product/fatal-contact/
Keneally, Thomas. The Commonwealth of Thieves: The Story of the First Fleet. Sydney:
Random House Australia, 2005. https://www.penguin.com.au/
Metcalfe, Tom. 2026. “British vial of smallpox scabs triggered the devastating 1789 outbreak among Indigenous Australians, study finds.” Live Science. livescience.com.
Nitschke, Matthew C., Alan N. Williams, Shane D. Ingrey, Billy Griffiths, Nicholas Pitt,
Lynette Russell, Sean Ulm et al. "Stochastic Models Indicate Rapid Smallpox Spread.
and Mass Mortality of Indigenous Australians after Colonial Exposure." Nature Human
Behavior (2026): 1-11. Accessed July 21, 2026. https://doi.org/10.1038/s41562-026-02504-6
Reynolds, Henry. The Other Side of the Frontier: Aboriginal Resistance to the European
Invasion of Australia. Sydney: UNSW Press, 2006. https://www.newsouthbooks.com.au/
