In 1789, one mysterious outbreak changed Australia's history; scientists may have solved it

One of the biggest mysteries in Australia's early colonial history may finally be closer to an answer. More than two centuries after a deadly epidemic swept through Aboriginal communities around Sydney, researchers say new evidence strongly supports the idea that the 1789 outbreak was caused by smallpox—not chickenpox or another unknown illness, as some historians have suggested over the years.

The epidemic unfolded just months after the First Fleet established the first British colony at Sydney Cove in 1788. Historical accounts describe a fast-moving disease that left victims with severe skin eruptions and claimed thousands of lives.

While the exact source of the infection remains one of history's most hotly debated questions, scientists say modern epidemiological analysis, combined with colonial records, is helping narrow the possibilities. The findings offer fresh insight into an event that permanently altered Australia's Indigenous communities and the country's colonial history.

Why has the 1789 outbreak remained such a mystery for more than 230 years?

The epidemic has puzzled historians because there are no confirmed biological samples from victims that can be tested with modern DNA technology. Instead, researchers have had to rely on journals, official reports and personal diaries written by British settlers and other witnesses.

Those historical descriptions consistently mention a disease that spread rapidly through Aboriginal communities around Port Jackson, causing fever, widespread pustules and unusually high death rates. Many communities had no previous exposure to European infectious diseases, making them especially vulnerable.

Over the decades, historians proposed several explanations. Some argued the illness was smallpox because of the distinctive skin lesions described in historical records. Others suggested chickenpox, citing the lack of definitive physical evidence. Without preserved viral material, neither theory could be conclusively proven.

The latest research revisits those records using modern disease modeling, comparing the documented symptoms, transmission patterns and mortality with what scientists know about historical outbreaks of both diseases.

What does the latest research reveal about the disease?

According to the new analysis, the outbreak's characteristics align much more closely with smallpox than chickenpox.

Researchers found that the speed of transmission, the severity of the illness and the exceptionally high mortality are all more consistent with smallpox epidemics recorded elsewhere during the 18th century. Chickenpox, while highly contagious, generally produces milder illness and is far less likely to devastate entire populations on the scale documented in 1789.

Scientists combined historical evidence with epidemiological modeling to test how each disease would likely have behaved under the conditions of early colonial Australia. Their findings suggest smallpox provides the strongest explanation currently supported by available evidence.

Even so, researchers emphasize that the conclusion is based on historical analysis rather than direct laboratory confirmation. Until viral DNA is recovered from archaeological remains—if that is ever possible—the diagnosis cannot be considered absolutely certain.

Where did the virus come from—and why is that question still unanswered?

Identifying the disease may be becoming easier, but identifying its origin remains one of Australia's greatest historical debates.

Several theories continue to be discussed by historians. One possibility is that the virus arrived with the First Fleet, either through infected people or contaminated materials carried from Britain. Another suggests visiting ships introduced the disease after settlement began. A third theory proposes that traders or sailors traveling through regional maritime routes may have unknowingly carried the virus before it reached Sydney.

Researchers say none of these explanations can yet be confirmed because historical documentation is incomplete. No surviving records clearly identify an infected person or trace the virus's movement into the colony.

As a result, scientists believe the evidence now points more confidently toward what the disease was than how it first arrived.

The 1789 epidemic reshaped Australia's history almost immediately.

Many historians estimate that the disease killed at least half of the Aboriginal population in parts of the Sydney region, dramatically reducing communities that had lived there for thousands of years. The loss of life disrupted family networks, leadership structures and the transmission of cultural knowledge at a pivotal moment in Australia's colonial expansion.

FAQs:

What caused the 1789 smallpox outbreak in Australia?

Researchers found that dried smallpox scabs carried by British First Fleet surgeons caused the 1789 outbreak. Doctors used these preserved scabs, stored in glass vials, for variolation—an early form of immunization.

How many Indigenous Australians died in the 1789 smallpox epidemic?

The epidemic killed between 40,000 and 220,000 Indigenous Australians. In the Sydney basin, mortality reached 50% to 70% among First Nations populations within months due to zero prior immunity.

Was smallpox intentionally brought to Australia by the British?

The study links the outbreak directly to the First Fleet's medical supplies, but it cannot prove if the release was intentional or accidental. While British colonial records don't document intentional release, Indigenous oral traditions and several historians suspect deliberate biological warfare.

How did scientists prove the First Fleet caused the outbreak?

Scientists from Flinders University and UNSW used computer spatial modeling to map disease transmission pathways. The models proved a northern transmission route from Indonesian traders was geographically impossible, pinpointing Sydney Harbor as ground zero.

Why couldn't live smallpox survive the voyage from Britain?

The First Fleet took eight months to reach Australia. Since active smallpox runs its course in 3 to 4 weeks, live infected passengers would have recovered or died at sea. Only dried variola scabs stored in sealed vials could remain infectious that long.