Joseph Hooker, while continuing to be a naval officer, worked at Kew for the next five years after which, through the patronage of the First Lord of the Admiralty, Lord Auckland, he left for India traveling in the same ship as the new Governor General, Lord Dalhousie. His Kew friend, Hugh Falconer, traveled out in the same party, on his way to take charge of the Saharanpur Botanic Garden. Later Joseph Hooker named three rhododendron species which he collected after these gentlemen: Rhododendron aucklandii (now known as R. griffithianum), R. dalhousiae (after Lady Dalhousie) and R. falconeri.
From Calcutta, Joseph Hooker travelled north to Sikkim and spent two years there exploring in the hills, based in Darjeeling where his host was Brian Hodgson, the British Resident in Nepal. Another friend was Dr. Archibald Campbell, the Superintendent of Darjeeling and Political Agent, Sikkim. Their help to him is recalled in the naming of Rhododendron hodgsonii, Magnolia campbellii and Rhododendron campbelliae (the latter after Mrs.. Campbell).
Dr. Thomas Thomson, an old college friend from Glasgow days, was then employed by the East India Company, and he accompanied Hooker on tours in the Khasia Hills, in Assam and in East Bengal. He is commemorated by R. thomsonii. Thomson collaborated with Joseph Hooker in the production of a Flora Indica. He later succeeded Dr. Wallich as Superintendent of the Calcutta Botanic Garden, about the same time as Joseph Hooker succeeded his father as Director of Kew.
Wallich had sent seed of R. arboreum and introduced R. campanulatum from Nepal in 1825. The closely related R. wallichii was named after him by Hooker.
Joseph Hooker's expedition is immortalised in his Rhododendrons of the Sikkim Himalaya published in three parts between 1849 and 1851, with thirty coloured plates, edited by Hooker's father. Before 1848, only thirty-three species of rhododendron were in cultivation; Hooker collected, sketched and described forty-three species of which thirty-six are still recognised as distinct.
Seed from his collections was grown on at Kew and seedlings were sent to friends in the west of Scotland, Wales and southwest England to tryout, notably to the Shilson family at Tremough near Penryn, to Robert Were Fox at Penjerrick and to Sir Charles lemon at Carclew. These formed the basis for the good quality hybrids that were made in Cornwall in the latter part of the 19th century, such as 'Shilsonii', 'Beauty of Tremough','Penjerrick','Barciayi' and 'Cornish Cross'. 'Sir Charles lemon' is usually regarded as a natural hybrid of R. arboreum and R. campanulatum.