John MacGillivray (18 December 1821 – 6 June 1867) was a Scottish naturalist, active in Australia between 1842 and 1867. MacGillivray was born in Aberdeen, the son of ornithologist William MacGillivray. He took part in three of the Royal Navy's surveying voyages in the Pacific. In 1842 he sailed as naturalist on board HMS Fly, despatched to survey the Torres Strait, New Guinea, and the east coast of Australia, returning to England in 1846. The standard author abbreviation J.MacGill. is used to indicate this person as the author when citing a botanical name.