Clayton was born in England, possibly in Fulham, Kent, in August 1695, and was the son of(ca. 1666–1737), who became early in 1714, and Lucy Clayton, whose maiden name is not known. He may have attended Eton College and the University of Cambridge, and like his father he might have studied law, but little is known for certain about his education. Clayton may have traveled to Virginia as early as 1715, but his name appears in extant colonial records for the first time on October 7, 1720, when he was identified as clerk of Gloucester County. He had probably worked as a deputy to Peter Beverley, who relinquished the position in 1719 or 1720, but the loss of the county records makes it impossible to determine for how long. Early in the 1720s Clayton married Elizabeth Whiting, daughter of Henry Whiting, a former member of the . Their three daughters and five sons included William Clayton, who became clerk of New Kent County and a member of the Conventions of 1776 and 1788.
As clerk of Gloucester County for more than fifty years, Clayton recorded deeds, land surveys, wills, and other documents and attended the county court sessions. He owned a 450-acre plantation, on which he raised tobacco and livestock, and eventually acquired more than thirty slaves. Clayton’s duties were not so onerous as to prevent him from devoting much of his energy to the study of botany. He provided Mark Catesby, a noted naturalist who had resided in Williamsburg off and on from 1712 to 1719, with at least one ornithological specimen and several plants, which Catesby mentioned in his Natural History of Carolina, Florida and the Bahama Islands (1731–1743). By 1735 Clayton had begun sending dried plant specimens to John Frederick Gronovius, a botanist of Leiden, in the Netherlands, often by way of Catesby. Initially Clayton asked Gronovius to identify the plants he sent, but Clayton soon began making his own identifications and was the first to name the genus Agastache, a group of perennial, woody herbs with spiked flowers. Gronovius shared Clayton’s specimens with Carolus Linnaeus, a Swedish botanist who developed the modern system of binomial nomenclature. In 1737 Linnaeus named the genus Claytonia, wildflowers of the Portulacaceae family, in Clayton’s honor.
During the 1730s Clayton traveled around Virginia collecting seeds and plants and began compiling for Gronovius a Catalogue of Herbs, Fruits, and Trees Native to Virginia, based on the new Linnaean system of classification. Without asking permission or informing Clayton of his intentions, Gronovius in 1739 translated the catalog into Latin and published it as Flora Virginica, a 128-page book describing about six hundred plant species. Clayton continued to identify and send specimens to Gronovius, who in 1743 published the second part of Flora Virginica, containing about three hundred additional species.
Clayton’s name became well known in American and European botanical circles, and by the 1740s he had begun a correspondence with the Pennsylvania botanist John Bartram that lasted for more than twenty years. They exchanged seeds and advice about the cultivation of native plants, many of which Clayton raised in his extensive garden, which Bartram described as one of the best he had seen in Virginia. In 1743 Bartram included Clayton, whom he considered a “worthy, ingenious man,” as a member of the American Philosophical Society, organized that year for the study of sciences and humanities. Clayton probably did not attend any of its meetings. On May 3, 1747, on the recommendation of Linnaeus, the Swedish Royal Academy of Science elected Clayton to membership.
Clayton continued collecting and in 1746 went to Canada and about 1747 or 1748 may have traveled as far west as the Mississippi River. About that time he began corresponding with Peter Collinson, an English horticulturalist and member of the Royal Society of London for Improving Natural Knowledge. They exchanged plant samples, and in the 1750s Clayton experimented with growing wheat from seed that Collinson provided. Collinson occasionally presented Clayton’s letters on scientific topics to the Royal Society and published one in the Gentleman’s Magazine in 1752 and another in 1755.
Known for the accurate detail of his plant descriptions, Clayton began compiling his own Flora Virginica during the mid-1750s and in 1758 sent Collinson a copy for publication. The volume was to include illustrations by Georg Dionysius Ehret, one of the foremost botanical artists of the period. Before Clayton’s illustrated version could be published, however, Gronovius’s son published a new edition of Flora in 1762, which apparently precluded any need for the new book. Clayton’s own copy was probably lost in 1787 when fire destroyed the clerk’s office in New Kent County, where his son had stored the botanist’s papers for safekeeping. The editions of Clayton’s Flora Virginica were the first, and for more than two hundred years the only, such compilation of Virginia’s native plants.
About 1769 Clayton hired John James Beckley, later clerk of the House of Representatives and librarian of Congress, to assist with the work in the county clerk’s office. Although his eyesight was failing, Clayton visited Orange County on a collecting expedition in the autumn of 1772, and his enthusiasm was such that he reportedly offered rewards to people who discovered native plants not yet known to him. In May 1773 he was elected the first president of the new Virginian Society for the Promotion of Usefull Knowledge, in effect a Virginia chapter of the American Philosophical Society.
John Clayton was in poor health when he wrote his will in October 1773, and he died, probably at his residence in Gloucester County, on December 15 of that year. His death was reported without comment in one of the Williamsburg newspapers three weeks later. In keeping with instructions, he was buried without ceremony or sermon next to the bodies of his wife and two of his children, probably at his plantation. In 1794 the English naturalist Sir Joseph Banks acquired hundreds of the specimens that Clayton had sent to Gronovius. They form the John Clayton Herbarium, part of the Natural History Museum in London.