In January 1866 he was appointed Professor of Natural History in the Royal Agricultural College, Cirencester, but resigned in June in consequence of being appointed by the Admiralty upon the recommendation of Joseph Dalton Hooker, to collect plants as naturalist on board under the command of Richard Charles Mayne, then commissioned for the survey of the Straits of Magellan and the west coast of Patagonia. This voyage started on 24 August 1866 from the Thames, and on 18 February 1967 she arrived in Port Stanley in the Falkland Islands to coal, departing again on 2 March, much to Cunningham's regret. They returned to the Falklands in 1868 enabling Cunningham to explore and study the plants and seaweeds on East Falkland returning a third time early in 1869. The Nassau returned to England on 31 July 1869 but Cunningham remained employed by the Navy so that he could write up his natural history notes and his narrative of the voyage, this was published in 1871 as he Natural History of the Straits of Magellan. In all, Cunningham published 18 scientific papers before 1872 his first on gannets was his theses but the others were mainly on his observations from voyage of the Nassau. He preented some of these papers to the Zoological Society of London and to the Linnean Society, becoming a fellow of the latter in 1870.
Queens College
In 1871 Cunningham was appointed Professor of Natural History at Queens College, Belfast where he spent the following 31 years as a university teacher. During his time in Belfast he was an enthusiastic naturalist, taught Botany, Geology and Zoology, ran excursions and had musen curation duties. He was not completely happy, complaining of overwork and of missing friends and family in Scotland. He unsuccessfully applied for a post at the University of Aberdeen in 1878. However, Cunningham remained to be highly regarded in Belfast and became involved in the University's administrative affairs. He was awarded an honorary degree by the Royal University of Ireland. While he was at Queens his mother donated some of the books from the library of her ancestor, Adam Smith, to the College's library.
Retirement
Cunningham gave talks to the Torquay Natural History Society in 1904 but he does not appear to have become a member. He died at Paignton on 14 July 1918.
