Banks' and Solander's specimens were studied aboard the HM Bark Endeavour by Sydney Parkinson. He drew each specimen and made notes on their colour, and for some species he completed watercolour illustrations. When they returned to London, Banks hired 5 artists to create watercolours of all of Parkinson's drawings. Between 1771 and 1784 Banks hired 18 engravers to create the copperplate line engravings from the 743 completed watercolours at a considerable cost. The Florilegium was not printed in Banks' lifetime and he bequeathed the plates to the British Museum.
Some of the plates were eventually printed. Between 1900 and 1905, James Britten and the British Museum issued prints of 315 of the plant engravings in black ink, under the title Illustrations of Australian Plants. Others were included in black and white in the 1973 book Captain Cook's Florilegium. The first complete full-colour edition of the Florilegium was published between 1980 and 1990 in 34 parts by Alecto Historical Editions and the British Museum. Only 100 sets were made available for sale, some on a subcription basis. The plates were printed using a 17th century technique known as à la poupée where each colour was applied directly to the plate, colour accuracy was checked against Parkinson's notes and through consultation with the Museum's botanist, Chris Humphries. Each plate took from one week to two months to proof. Parts 1 to 15 consist of 227 plates relating to the Australian flora, parts 16 to 34 include South America and other Pacific locations.
A documentary recounting the journey and the publication of the Florilegium, Banks' Florilegium: The Flowering of the Pacific, was released in 1984. It was narrated by Australian Robert Hughes. A book on the subject, The flowering of the Pacific: Being an account of Joseph Banks' travels in the South Seas and the story of his Florilegium, by Brian Adams was published by the British Museum in 1986.