In 1851 he married Frances Harriet Henslow (1825 – 1874), daughter of John Stevens Henslow. They had four sons and three daughters. After his first wife's death in 1874, in 1876 he married Hyacinth Jardine (1842 – 1921), daughter of William Samuel Symonds and the widow of Sir William Jardine. They had two sons.

Joseph Hooker died in his sleep at midnight at home on 10 December 1911 after a short and apparently minor illness. The Dean and Chapter of Westminster Abbey offered a grave near Darwin's in the nave but also insisted that Hooker be cremated before. His widow, Hyacinth, declined the proposal and eventually Hooker's body was buried, as he wished to be, alongside his father in the churchyard of St. Anne's Church, Kew, on Kew Green, within short distance of Kew Gardens.

Hooker Oak in Chico, California, was named after him.

In 1845, Hooker applied for the Chair of Botany at the University of Edinburgh. This position included duties at the Royal Botanic Gardens of Scotland, and so the appointment was influenced by local politicians. An unusually protracted struggle ensued, resulting in the election of the locally born and bred botanist, John Hutton Balfour. The Darwin correspondence, now public, makes clear Darwin's sense of shock at this unexpected outcome. Hooker declined a chair at Glasgow University which became vacant on Balfour's appointment. Instead, he took a position as botanist to the Geological Survey of Great Britain in 1846. He began work on palaeobotany, searching for fossil plants in the coal beds of Wales. He became engaged to Frances Henslow, daughter of Charles Darwin's botany tutor John Stevens Henslow, but he was keen to continue to travel and gain more experience in the field. He wanted to travel to India and the Himalayas. In 1847 his father nominated him to travel to India and collect plants for Kew.

When Hooker returned to England, his father had been appointed director of the Royal Botanic Gardens, Kew, and so was now a prominent man of science. William Hooker, through his connections, secured an Admiralty grant of £1000 to defray the cost of plates for his son's Botany of the Antarctic Voyages, and an annual stipend of £200 for Joseph while he worked on the flora. Hooker's flora was also to include that collected on the voyages of Cook and Menzies held by the British Museum and collections made on the Beagle. The floras were illustrated by Walter Hood Fitch (trained in botanical illustration by William Hooker), who would go on to become the most prolific Victorian botanical artist.

Hooker's collections from the voyage were described eventually in one of two volumes published as the Flora Antarctica (1844 – 47). In the Flora he wrote about islands and their role in plant geography: the work made Hooker's reputation as a systemist and plant geographer. His works on the voyage were completed with Flora Novae - Zelandiae (1851 – 53) and Flora Tasmaniae (1853 – 59).

The 1839 Antarctic expedition consisted of two ships, HMS Erebus and HMS Terror; it was the last major voyage of exploration made entirely under sail. Hooker was the youngest of the 128 man crew. He sailed on the Erebus and was assistant to Robert McCormick, who in addition to being the ship's Surgeon was instructed to collect zoological and geological specimens. The ships sailed on 30 September 1839. Before journeying to Antarctica they visited Madeira, Tenerife, Santiago and Quail Island in the Cape Verde archipelago, St Paul Rocks, Trinidade east of Brazil, St Helena, and the Cape of Good Hope. Hooker made plant collections at each location and while travelling drew these and specimens of algae and sea life pulled aboard using tow nets.

From the Cape they entered the southern ocean. Their first stop was the Crozet Islands where they set down on Possession Island to deliver coffee to sealers. They departed for the Kerguelen Islands where they would spend several days. Hooker identified 18 flowering plants, 35 mosses and liverworts, 25 lichens and 51 algae, including some that were not described by surgeon William Anderson when James Cook had visited the islands in 1772. The expedition spent some time in Hobart, Van Diemen's Land, and then moved on to the Auckland Islands and Campbell Island, and onward to Antarctica to locate the South Magnetic Pole. After spending 5 months in the Antarctic they returned to resupply in Hobart, then went on to Sydney, and the Bay of Islands in New Zealand. They left New Zealand to return to Antarctica. After spending 138 days at sea, and a collision between the Erebus and Terror, they sailed to the Falkland Islands, to Tierra del Fuego, back to the Falklands and onward to their third sortie into the Antarctic. They made a landing at Cockburn Island and after leaving the Antarctic, stopped at the Cape, St Helena and Ascension Island. The ships arrived back in England on 4 September 1843; the voyage had been a success for Ross as it was the first to confirm the existence of the southern continent and chart much of its coastline.

On 11 November 1847 Hooker left England for his three year long Himalayan expedition; he would be the first European to collect plants in the Himalaya. He received free passage on HMS Sidon, to the Nile and then travelled overland to Suez where he boarded a ship to India. He arrived in Calcutta on 12 January 1848, then travelled by elephant to Mirzapur, up the Ganges by boat to Siliguri and overland by pony to Darjeeling, arriving on 16 April 1848.

Hooker's expedition was based in Darjeeling where he stayed with naturalist Brian Houghton Hodgson. Through Hodgson he met British East India Company representative Archibald Campbell who negotiated Hooker's admission to Sikkim, which was finally approved in 1849 (He was to be briefly taken prisoner by the Raja of Sikkim). Meanwhile, Hooker wrote to Darwin relaying to him the habits of animals in India, and collected plants in Bengal. He explored with local resident Charles Barnes, then travelled along the Great Runjeet river to its junction with the Tista River and Tonglu mountain in the Singalila range on the border with Nepal.

Hooker and a sizable party of local assistants departed for eastern Nepal on 27 October 1848. They travelled to Zongri, west over the spurs of Kangchenjunga, and north west along Nepal's passes into Tibet. In April 1849 he planned a longer expedition into Sikkim. Leaving on 3 May, he travelled north west up the Lachen Valley to the Kongra Lama Pass and then to the Lachoong Pass. Campbell and Hooker were imprisoned by the Dewan of Sikkim when they were travelling towards the Chola Pass in Tibet. A British team was sent to negotiate with the king of Sikkim. However, they were released without any bloodshed and Hooker returned to Darjeeling where he spent January and February 1850 writing his journals, replacing specimens lost during his detention and planning a journey for his last year in India.

Reluctant to return to Sikkim, and unenthusiastic about travelling in Bhutan, he chose to make his last Himalayan expedition to Sylhet and the Khasi Hills in Assam. He was accompanied by Thomas Thompson, a fellow student from Glasgow University. They left Darjeeling on 1 May 1850, then sailed to the Bay of Bengal and travelled overland by elephant to the Khasi Hills and established a headquarters for their studies in Churra where they stayed until 9 December, when they began their trip back to England.

Hooker's survey of hitherto unexplored regions, the Himalayan Journals, dedicated to Charles Darwin, was published by the  Calcutta Trigonometrical Survey Office in 1854, abbreviated again in 1855 and later by (The Minerva Library of Famous Books) Ward, Lock, Bowden & Co., 1891.

The 1860 Palestine trip was taken in the autumn of 1860, with Daniel Hanbury. They visited and collected in Syria and Palestine; no full length report was published, but a number of papers were written. Hooker recognised three phytogeograpical divisions: Western Syria and Palestine; Eastern Syria and Palestine; Middle and Upper mountain regions of Syria.

Hooker visited Morocco from April to June 1871, in the company of John Ball, George Maw and a young gardener from Kew, called Crump.

The 1877 Western Unites States trip was undertaken with his friend Asa Gray, the leading American botanist of the day. They wished to investigate the connection between the floras of eastern United States and those of eastern continental Asia and Japan; and the line of demarkation between Arctic floras of America and Greenland. As probable causes they considered the Glacial periods and an earlier land connection with an Arctic continent. "A difficult question was why in the great mountain chains of the Western United States there appeared to be only a few botanical enclaves of plants of eastern Asiatic afinities among plants of Mexican and more southern types."

Hooker visited a number of cities and botanical institutions before moveing west and climbing to 9,000 ft to camp at La Veta. From Fort Garland they climbed the Sierra Blanca at 14,500 ft. After returning to La Veta, they went beyond Colorado Springs to Pike's Peak. Next to Denver and Salt Lake City for an excursion into the Wasatch mountains. A journey of 29 hours took them to Reno and Carson City, then Silver City and ten days by wagon across the Sierra Nevada. Thus they came to the Yosemite and Calaveras Grove, and ended up in San Francisco. Hooker was back in Kew with 1,000 dried specimens by October.

Some idea of the delights he encountered (trivia from his journal & letters):

• Hooker met and talked to Brigham Young, whom he described as respectable and well spoken. The new religion did not meet with Hooker's approval: "All the school children are brought up to believe in him [Brigham Young], and in a lot of scripture history as useless and idle as that taught in our schools."

• Of Georgetown: the "finger tip of civilisation" where "the people sleep without locks to their doors, the fire engines are well manned and in capital order, and there is no end of food".

• "The New Englanders are most like us in language, speech and habits... The Americans are great and promiscuous eaters... beds are remarkably clean and good, but the pillows are too soft."

His views on the flora of Colorado and Utah: There are two temperate, and two cold or mountain floras, viz: 1. a prairie flora derived from the eastward; 2. a so-called desert and saline flora derived from the west; 3. a sub-alpine; 4. an alpine flora, the two latter of widely different origin, and in one sense proper to the Rocky Mountain ranges.

His overview of North American flora contained these elements:

Polar area, from the Behring Strait to Greenland.

British North American flora, south of the Arctic flora, in five meridional belts.

United States flora, in belts:

The Great Eastern Forest region, from the Atlantic to beyond the Mississippi.

The Prairie region.

The Sink region, confined to gullies of the mountains.

The Sierra Nevada.