The 26th July, 1851, found him at Tonga Taboo, in the Friendly Islands, revelling in his first glimpse of nature in mid-Pacific. The fringing reef proved somewhat disappointing, for amid the multitudinous and many-coloured animal forms only a few green Algae were to be found. Harvey spent six months in the Pacific, visiting island after island according as the mission boats supplied a means of transport, collecting seaweeds and a good many marine animals. At that time social conditions in the South Seas were very different from what they are now. The adjoining Fiji Island group, for instance, was still in a savage state: the captain of the mission vessel told Harvey how, only four years before, he had seen one hundred human bodies laid out for a great feast, and cannibalism was still a habitual practice there; but the Friendly Islands, though but recently in a similar condition, seem already to have deserved their name, and Harvey's experiences of the natives, with whom he was much in contact, appear to have been of the pleasantest description; in Fiji also, where several weeks were spent, the founding of a Christian mission (permitted only two years before after eighteen years' refusal) had already greatly altered local practices; devil-worship and cannibalism were rapidly dying out. Harvey, applying at the mission station for a responsible guide, was furnished with a man entitled "Koroe," which, it appeared, was an honourable title "something equivalent to a C.B. in England," and bestowed only on a person who had committed at least five murders. Harvey returned to Sydney, and thence to Europe by Valparaiso and Panama, having a severe bout of fever on the way. He reached home in October, 1856, after an absence of over three years.
Here an important change of life awaited him. G. J. Allman succeeded to the Natural History chair in Edinburgh, rendered vacant by the death of Edward Forbes, and Harvey was elected to the chair in Trinity College, Dublin, the difficulties which led to his rejection twelve years earlier being not raised on this occasion, though the law remained the same. At the same time, the incorporation of the several Dublin Society professorships in the newly founded Museum of Irish Industry (now the Royal College of Science for Ireland), gave him additional work, as his post was converted into a Natural History and Economic chair. However, the considerable increase of lecturing and teaching thus brought upon him did not prevent his pushing on vigorously with the now large arrears of phycological work. His first action was to finish and publish the third and last section of the _Nereis Boreali-Americana_ and then bring to a conclusion his enumeration of the seaweed flora of North America. This was accomplished in 1858, and in the same year he began the publication of the results of his work in Australia. The _Phycologia Australica_, which was issued in parts during the ensuing five years, ran to five volumes, each containing sixty coloured plates, and descriptions of all the species known from Australasian waters. In the year following the launching of this work, he commenced the publication of two important treatises on the phanerogamic flora of South Africa. In the first of these, the well-known _Flora Capensis_, he had the co-operation of Dr O. W. Sonder of Hamburg. This extensive work he did not live to complete; the third volume, which ran as far as the end of the Campanulaceae, being published the year before his death. The other work was his _Thesaurus Capensis_, a series of plates of rare or interesting South African plants, designed to supplement and illustrate the unillustrated _Flora_; of this he lived to issue only two volumes, each containing one hundred plates.