The botanical fruits of the three years he thus spent in the Southern Seas were the two volumes of Flora Antarctica (1844–47), Flora Novae-Zelandiae (1851–53) and Flora Tasmaniae (1853–59), which he published on his return. He had come across some fossil plants found during his travels. Through a good word of his father, he was appointed botanist to the Geological Survey of Great Britain in 1846. he would stay interested in palaeobotany till the end of his life.

His next expedition was to the northern frontiers of India (1847–51), and the expenses in this case also were partially defrayed by the government. The party had its full share of adventure. Hooker and his friend Dr Archibald Campbell were detained in prison for some time by the Raja of Sikkim, but nevertheless they were able to bring back important results, both geographical and botanical.

Their survey of hitherto unexplored regions, the Himalayan Journals, dedicated to Charles Darwin,was published by the Calcutta Trigonometrical Survey Office. He then started the series Flora Indica in 1855, together with Thomas Thompson. Their botanical observations and the publication of the Rhododendrons of Sikkim-Himalaya (1849–51), formed the basis of elaborate works on the rhododendrons of the Sikkim Himalaya and on the flora of India. His works were illustrated with lithographs by Walter Hood Fitch.

In 1859 he published the Introductory Essay to the Flora Tasmaniae, the final part of the Botany of the Antarctic Voyage. It was in this essay (which appeared just one month after the publication of Charles Darwin's "On the Origin of Species"), that Hooker announced his support for the theory of evolution by natural selection, thus becoming the first recognised man of science to publicly back Darwin.

Among other journeys undertaken by Hooker were those to Palestine (1860), Morocco (1871), and the United States (1877), all yielding valuable scientific information. In the midst of all this travelling in foreign countries he quickly built up for himself a high scientific reputation at home. In 1855 he was appointed assistant-director of the Royal Botanic Gardens, Kew, and in 1865 he succeeded his father as full director, holding the post for twenty years. Under the directorship of father and son Hooker, the Royal Botanical gardens of Kew rose to world renown.

At the early age of thirty he was elected a fellow of the Royal Society, and in 1873 he was chosen its president (till 1877). He received three of its medals: the Royal in 1854, the Copley in 1887 and the Darwin in 1892. His greatest botanical work was the Flora of British India, published in seven volumes between 1872 and 1897.

He acted as president of the British Association at its Norwich meeting of 1868, when his address was remarkable for its championship of Darwinian theories. Of Darwin, indeed, he was an early friend and supporter: it was he who, with Charles Lyell, first induced Darwin to make his views public, and the author of The Origin of Species recorded his indebtedness to Hooker's wide knowledge and balanced judgment.

He was the author of numerous scientific papers and monographs, and his larger books included, in addition to those already mentioned, a standard Students Flora of the British Isles and a monumental work, the Genera plantarum (1860–83), based on the collections at Kew, in which he had the assistance of George Bentham.

On the publication of the last part of his Flora of British India in 1897 he was created GCSI, of which order he had been made a knight commander twenty years before; and ten years later, on attaining the age of ninety in 1907, he was awarded the Order of Merit. In 1904, at the age of 87, he published A sketch of the Vegetation of the Indian Empire.

Joseph Hooker died on 10 December 1911. His wife declined the proposal of a burial of his body in Westminster Abbey alongside Darwin.

Hooker Oak in Chico, California is named after him.