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- Narrative of the Surveying Voyages of Her Majesty's Ships 'Adventure' and 'Beagle' between the years 1826 and 1836, describing their examination of the Southern shores of South America, and the 'Beagle's' circumnavigation of the globe. (1839)
- The Structure and Distribution of Coral Reefs. Being the First Part of the Geology of the Voyage of the Beagle. (1842)
- Geological observations on Coral Reefs, Volcanic Islands, and on South America: being the Geology of the Voyage of the Beagle, under the Command of Capt. FitzRoy, during the Years 1832-36. (1842-1846)
- Journal of Researches into the Natural History and Geology of the countries visited during the Voyage of H.M.S. 'Beagle' round the world, under the command of Captain Fitz-Roy, R.N. (1845)
- A Monograph of the Fossil Lepadidae; or, Pedunculated Cirripedes of Great Britain. (1851)
- A Monograph of the Sub-class Cirripedia, with Figures of all the Species. The Lepadidae; or, Pedunculated Cirripedes. (1851)
- A Monograph on the Fossil Balanidę and Verrucidę of Great Britain. (1854)
- Monograph of the Sub-class Cirripedia, with Figures of all the Species. The Balanidae (or Sessile Cirripedes); the Verrucidae, etc. (1854) Die Entstehung der Arten (On the origin of species by means of natural selection., 1859)
- On the various contrivances by which British and foreign orchids are fertilised by insects. (1862)
- The variation of animals and plants under domestication. (1868)
- The descent of man and selection in relation to sex. (1871)
- The expression of the emotions in man and animals. (1872)
- The movements and habits of climbing plants. (1875)
- Insectivorous plants. (1875)
- The effects of cross and self-fertilisation in the vegetable kingdom. (1876)
- The different forms of flowers on plants of the same species. (1877)
- The power of movement in plants. (1880)
- The formation of vegetable mould, through the action of worms. (1881)
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