Doctor Milligan was born in Scotland and died in London. He spent thirty years of his remarkably productive life in Tasmania, then known as Van Diemen’s Land. He can be described as a Renaissance man, working in fields as various as botany, geology, medicine (he was a surgeon), prospecting, mining, public administration and a general promotion of science. Milligan was associated with many prominent personalities of his time, including the famous botanist and explorer Joseph Dalton Hooker, botanist and politician Ronald Campbell Gunn, as well as Lady Franklin and Sir John Franklin, who was Governor of Tasmania (1837-1843). The Franklins presided over something akin to a little Renaissance in this small colony, supporting all forms of art, science and exploration.

Milligan arrived in Tasmania in 1831, when the colony was embroiled in the upheaval of the Black War. Some historians question the appropriateness of this term, but it aptly reflects the situation in the late 1820s and the early 1830s. When the European settlers moved to acquire more arable land, the simmering conflict with Aboriginal Tasmanians erupted into full scale hostilities. The European quest for land was met with a tenacious armed resistance. The colony enacted martial law and made a coordinated, military-style effort to achieve, what in Charles Darwin’s words was ‘the great advantage of being free from a native population.’ Protracted conflicts and the violent culmination of war shattered the Aboriginal population and the prospect for independent life had vanished. But the war was inconclusive and so since the early 1830s nearly all 200 surviving Aboriginal people were persuaded to surrender and by 1835 deported to Flinders Island in Bass Strait.

In the parlance of the time, the Aborigines on Flinders Island were to be ‘civilized and Christianized.’ In practice they were not equipped with the living skills to function in oppressive detention. Scanty resources were provided for basic necessities such as food, shelter, hygiene and medical care. Even Milligan, a man with humanitarian inclination and genuine interest in Aboriginal culture, could not understand that the major problem for the inmates was lack of autonomy. Aborigines were unable to live an imposed white-man’s lifestyle, nor were they allowed to live off the land in their traditional manner. And so, in a little over a decade, more than 150 people died and there were virtually no children left.

In 1843 Milligan was appointed superintendent and medical officer of the Aborigines imprisoned on Flinders Island. For a brief period of 12 months in 1846-47 he was visiting magistrate and medical officer of the penal settlement at Macquarie Harbour, after which he returned to his duties. In 1847 he supervised the return of forty-six surviving Aborigines to the Tasmanian mainland, where they were placed at Oyster Cove camp, south of Hobart, facing North Bruny Island. He continued in these roles until 1855. In this time Milligan produced an extensive 'Vocabulary of the Dialects of Some of the Aboriginal Tribes of Tasmania', published by the Royal Society of Tasmania in 1859. This work provides quite rare documentation of languages and customs of Aboriginal Tasmanians. He also assembled a small collection of artefacts, few of which made their way to the Australian Museum’s collection.

Tasmania became a colony, independent from New South Wales, in December 1825.