In 1837, a year after the Beagle returned to England, Darwin started a clandestine notebook, which concerned itself with his thoughts on "transmutation" and "origins", i.e., the larger implications of his and others' observations on animals and plants. This eventually grew to many volumes, but he never showed it to other naturalists. Eventually, in letters and conversations with friends he hoped would not be too shocked, he began to reveal the trend of his thinking. In 1852, after publishing several large volumes of his meticulous observations on barnacles, both living and fossil, he began sorting his notes on species and what he had decided to call "natural selection". This went on slowly, but chapter had begun to pile on chapter, when in 1858 a letter arrived from another naturalist, Alfred Russel Wallace, proposing many of the same ideas, albeit on thinner evidence. Darwin was immediately concerned with his priority and greatly hurried the completion of his book. It was published in 1859 as "On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life."

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Darwin had no fancy scientific tools beyond a simple microscope. His observations were confined to what he could see of plants and animals with the unaided senses. He had no knowledge of genetics; Gregor Mendel published his first paper on breeding experiments in peas six years after Origin and his papers were not appreciated for another 30 years or more. Although bacteria were known to exist, the germ theory of disease was yet to be proposed. Nevertheless, Darwin got it right. He marshaled evidence from domestic breeding of pigeons (a specific interest of his), sheep, cattle, dogs, cabbages and gooseberries. In each case, man's selection of desired natural variations of the species resulted in startling transformations. He believed that such variations occur naturally at random, and are inheritable. Transferring to undomesticated nature, he demonstrated that competition for food, growing space, the necessities of life, constitute a powerful selective force toward whatever variations benefit survival. He called this "natural selection". He spent a chapter demonstrating that geological findings show the earth to be millions of years old and constantly subject to gradual change over that time. He examined fossils of extinct animals and noted their relationship to living species. He discussed that embryos, growing toward their final organization, often temporarily resemble more primitive animals. The only illustration in his book was a branching diagram showing how a simple progenitor over the stretch of geological time could result in numerous species.

The depth and breadth of Darwin's evidence won over most, although not all, scientists of the day. The rest of the interested public was a different story. Darwin knew that his ideas would stir up intense controversy. His grandfather, Erasmus Darwin, had been a noted freethinker, publicly discarding both Bible and Christ as irrelevant. His other grandfather, Josiah Wedgwood, was a prominent Unitarian, a faith that honors Christ as a prophet but rejects both the Trinity and the divinity of Christ. Such beliefs were anathema to the established church of England. Suddenly, there entered Charles Darwin's new theory. Many adherents of the Anglican Church saw the theory as a denial of both the Bible and church tradition. They repeatedly attacked Darwin as a Devil's disciple. Furthermore, politicians believed such beliefs would encourage revolution against crown and established order. Nevertheless, there were liberal clerics who rushed to defend the theory.

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