The Structure and Distribution of Coral Reefs, Being the first part of the geology of the voyage of the Beagle, under the command of Capt. Fitzroy, R.N. during the years 1832 to 1836, was published in 1842 as Charles Darwin's first monograph, and set out his theory of the formation of coral reefs and atolls. He conceived of the idea during the voyage of the Beagle while still in South America, before he had seen a coral island, and wrote it out as HMS Beagle crossed the Pacific Ocean, completing his draft by November 1835. At the time there was great scientific interest in the way that coral reefs formed, and Captain Robert FitzRoy's orders from the Admiralty included the investigation of an atoll as an important scientific aim of the voyage. FitzRoy chose to survey the Keeling Islands in the Indian Ocean. The results supported Darwin's theory that the various types of coral reefs and atolls could be explained by uplift and subsidence of vast areas of the Earth's crust under the oceans.
The book was the first volume of three Darwin wrote about the geology he had investigated during the voyage, and was widely recognised as a major scientific work that presented his deductions from all the available observations on this large subject. In 1853, Darwin was awarded the Royal Society's Royal Medal for the monograph and for his work on barnacles. Darwin's theory that coral reefs formed as the islands and surrounding areas of crust subsided has been supported by modern investigations, and is no longer disputed, while the cause of the subsidence and uplift of areas of crust has continued to be a subject of discussion.
When the Beagle set out in 1831, the formation of coral atolls was a scientific puzzle. Advance notice of her sailing, given in the Athenaeum of 24 December, described investigation of this topic as "the most interesting part of the Beagle's survey" with the prospect of "many points for investigation of a scientific nature beyond the mere occupation of the surveyor. In 1824 and 1825, French naturalists Quoy and Gaimard had observed that the coral organisms lived at relatively shallow depths, but the islands appeared in deep oceans. In books that were taken on the Beagle as references, Henry De la Beche, Frederick William Beechey and Charles Lyell had published the opinion that the coral had grown on underwater mountains or volcanoes, with atolls taking the shape of underlying volcanic craters. The Admiralty instructions for the voyage stated: