The eleven-month journey to Tasmania and from there to the Great Ice Barrier

There were stops at various islands including Madeira, the first port-of-call, then a nine-week stay at the Cape of Good Hope and on to Kerguelen Island for a nine-week stay. Joseph Hooker studied its flora intensively and increased the number of plants known there to 150, which included lichens and seaweeds. The expedition made good use of the Kerguelen "cabbage", Pringlea antiscorbutica, which Cook had found to be effective in preventing scurvy. It was abundant there and was used as the sole vegetable for the crew for four months. Joseph Hooker's Flora Antarctica contains the first published description of the Kerguelen cabbage, which, like the true cabbage, Brassica oleracea, is in the family Cruciferae. From Kerguelen Island to Tasmania they encountered atrocious weather, and one of the crew was swept overboard. After a three-month stay in Tasmania, where Joseph learnt that his brother William, a doctor, had died of yellow fever in Jamaica, the ships headed south. They visited Auckland Island, which Joseph had time to thoroughly botanise, and then made a brief call at Campbell Island. Finally, they reached Victoria Land in Antarctica and located the precise bearing of the South Magnetic Pole (160 miles inland). They discovered Mt Erebus (3,798 metres) on the fringes of what is now the Ross Sea. As Joseph wrote to his father:

To see the dark cloud of smoke tinged with flame rising from the volcano in one column, one side jet black and the other reflecting the colors [sic] of the sun, turning off at a right angle by some current of wind and extending many miles to leeward; it is a sight far exceeding anything I could imagine and which is very much heightened by the idea that we have penetrated far farther page 75 than was once thought practicable, and there is a sort of awe that steels over us all in considering our total insignificance and helplessness.

Three months stay in Tasmania, a visit to Sydney, then a three-month say in New Zealand, a trip to the Falklands and another visit to the Ice Barrier

The Erebus and Terror then returned to Tasmania.

The ships reached Paihia in the Bay of Islands on 16 August 1841. There Hooker met William Colenso (1811-99), printer, missionary, school inspector and botanist. Colenso was of considerable help to Hooker in his botanical trips and himself benefited from Joseph's advice and encouragement. Joseph named Colensoa physaloides after him, but this plant is now known as Pratia physaloides (Plate 29). The expedition remained in the Bay of Islands throughout their New Zealand visit, and a considerable amount of time was spent in obtaining suitable spars for the ships. Just before they left New Zealand, Joseph received a letter from his father informing him of his appointment to Kew, a fact that Joseph had read in a newspaper in Sydney three months before. Ross and his crews then went south to the Chatham Islands and on to the pack ice, where they struggled for forty-six days to get clear of it. Both ships were damaged, not only by ice, for they collided and were locked together for a time. The Terror was in the worst condition, for a fire broke out and was only extinguished by partly flooding the hold. Eventually they reached the Falkland Islands in April 1842.

A six-month stay in the Falklands, some excursions, and the four-month homeward voyage

The ships were soon hauled ashore for repairs. Intensive botanising on the Falklands yielded only some 100 species of flowering plants for Joseph. Seeds of a tussock grass he collected and sent to Kew later proved useful, as the grass was successfully introduced to the Shetland Islands for animal fodder. The Erebus and Terror visited Hermite Island, part of Tierra del Fuego, near Cape Horn, which Joseph was particularly interested in seeing, for Charles Darwin had been there on the Beagle. Joseph met Darwin not long before the Antarctic voyage began and had a copy of his Journal of Researches into the Geology and Natural History of the Various Countries Visited by H.M.S. Beagle, which he often referred to, on board. The two men subsequently became life-long friends. Darwin's surviving letters to Hooker, when typed out, run to over 800 pages. After the voyage, Joseph had been fully informed of Darwin's ideas on evolution and natural selection and had faithfully kept them secret many years before the publication in 1859 of The Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life.

Hermite Island proved to be richer in mosses than any comparably sized region Joseph ever visited, and he collected more than 100 different species. Tierra del Fuego had an interesting flora, with some flowering plants very similar to English ones and many lichens identical to those found in Britain. This region seemed to him the "great botanical centre of the Antarctic Ocean", and many of his ideas on geographical plant distribution and dispersal were fostered by this visit. In December 1842 they left the page 76 Falklands and headed south once more. The ships narrowly escaped being frozen in the ice. Joseph Hooker found on one of the Antarctic islands a lichen, which he found again high in the Himalayas. James Ross was able to confirm that there was only one South Magnetic Pole, and by April 1843 the ships had reached the Cape of Good Hope. In September the voyage was over.