One year after the first fleet arrived in 1788, there was a devastating outbreak of smallpox among the local aboriginal people, killing up to about half of the people and also spreading to other groups.

According to accounts of the time, there were no cases of smallpox among the white population and there had been none on the ships so it was a mystery as to how smallpox had infected the aboriginal people.

Captain Arthur Phillip, the first governor, wrote letters back to England where he discussed the smallpox outbreak and theorized that it may either have already existed in Australia (it didn't) or that it may have been brought on the French ships (the two ships Astrolabe and Boussole under the command of Captain La Perouse).

"Whether the small pox, which has proved fatal to great numbers of the natives, is a disorder to which they were subject before any Europeans visited the country, or whether it was brought by the French ships, we have not yet attained sufficient knowledge of the language to determine. It never appeared on board any of the ships in our passage, nor in the settlement, until some time after numbers of the natives had been dead with the disorder."

However, the French ships arrived at the same time as the first fleet and didn't stay long, and smallpox was not observed until the outbreak 1 year later, which is outside the contagion period.

European medicine of the day practiced a form of inoculation called 'variolation" where healthy people are infected by material from an infected person (scabs or pus) in order to produce a milder infection and provide immunity. The surgeons of the colony were most likely carrying vials of smallpox material to be used for variolation. That could may well have been the source of the infection, though that has been denied and challenged.

There is also another theory that smallpox was introduced from the north of Australia through the Macassan trepangers from the Indonesian archipelago who traded with aboriginal bands in northern Australia for sea slugs. This paper argues against that theory.