John Clarkson Jay (11 September 1808 New York City - 15 November 1891 Rye, New York) was a United States physician and conchologist.
He was the son of Peter A. Jay and grandson of John Jay, diplomat and first Supreme Court chief justice. He graduated from Columbia in 1827, and at the College of Physicians and Surgeons in 1831. In addition to his practice of medicine, he made a specialty of conchology, and acquired the most complete and valuable collection of shells in the United States. This and his costly library on this branch of science were purchased by Catherine Wolfe and presented, in memory of her father, to the American Museum of Natural History, where it is known as the Jay Collection. In 1832 he became a member of the Lyceum of Natural History (now New York Academy of Sciences), and was its treasurer 1836-1843. He took an active part in the efforts that were made during that time to obtain subscriptions for the new building, and bore the principal burden in planning and superintending its construction.
He was one of the founders of the New York Yacht Club, and for some time its secretary. From 1859 until 1880, he was a trustee of Columbia College. The shells collected by the expedition of Com. Matthew C. Perry to Japan were submitted to him for examination, and he wrote the article on that subject in the government reports. Jay wrote Catalogue of Recent Shells (New York, 1835), Description of New and Rare Shells (1836), and later editions of his catalogue, in which he enumerates about 11,000 well-marked varieties, and at least 7,000 well-established species.