This paper provides a biography, bibliography and taxonomic catalog for John Clarkson Jay (1808–1891), emphasizing his malacological research based upon his sizable collection and his contributions to the growth and expansion of the New York Lyceum of Natural History, the predecessor to the American Museum of Natural History. Jay described one new genus and 49 new species of molluscs; type specimens are known for 34 of them. He also published but did not describe 76 manuscript names mostly from material collected by Nuttall, of which 28 were made available by later authors (mostly by either Reeve or Carpenter). His collection and sizable library of rare books formed the nucleus of the malacological collection and the rare book library of the American Museum of Natural History. This paper summarizes his life, the growth of his collection, his publications, his new taxa, and his broader role in 19th-century New York professional life.