Baldwin conducted correspondence with many notable thinkers of his time, including Ralph Waldo Emerson, Charles Darwin, James Russell Lowell, and particularly his friend Charles Sumner. He accepted Darwin's theory of evolution while maintaining a belief in the divine origin of "first forms." In 1865 he was elected a corporate member of the American Oriental Society. Baldwin's anthropological writing posited the origins of human civilization as arising among an Arabian or Northeast African people, the Cushites, in pre-historic times. In Ancient America, In Notes on American Archaeology he also speculated on the origins of the "Mound Builder" people then believed to have constructed the famous mounds around the Mississippi and Ohio River Valleys, suggesting that they had been an aboriginal people who had migrated northwards from Central America or Mexico. He rejected the then-common notion that they had been a lost European, Semitic, or Asiatic people who had been wiped out by the North American Indians, asserting on the contrary that the Mounds were "wholly original, wholly American" and "did not come from the Old World". He did, however, still subscribe to the idea that these "Mound Builders" were not the same as the American Indian inhabitants of the region at that time, who he believed were a separate race originating in Asia.
Works
A scriptural view of the Messiah: Being the substance of a sermon delivered in the Methodist chapel, Dighton, Mass., on Sunday evening, May 27, 1832, Edmund Anthony, Office of Independent Gazette, 1832.
Lessons from the grave: A discourse delivered in North Branford, June 12, 1842, and occasioned by the death of Daniel Wheadon, Hitchcock & Stafford, 1842.
The story of Raymond Hill,: And other poems, W.D. Ticknor & Co, 1847.
Congress and Reconstruction: Speech of Hon. John D. Baldwin of Massachusetts in the House of Representatives, April 7, 1866, 1866.
Human rights and human races, Congressional Globe Office, 1868.
Human rights and human races : speech of Mr. Baldwin, of Massachusetts, delivered in the House of Representatives, January 11, 1868, in reply to a speech of Hon. James Brooks, of New York, on the Negro race., F. & J. Rives & G.A. Bailey, 1868.
Pre-Historic Nations; or, Inquiries Concerning Some of the Great Peoples and Civilizations of Antiquity, New York, Harper, 1869,.
Ancient America, in notes on American archæology, New York, Harper, 1871,.
A record of the descendants of John Baldwin, of Stonington, Conn.: With notices of other Baldwins who settled in America in early colony times, Tyler & Seagrave, 1880.
Thomas Stanton of Stonington, Conn: An incomplete record of his descendants, Tyler & Seagrave, 1882.
A record of the descendants of Capt. George Denison of Stonington, Connecticut: With notices of his father and brothers, and some account of other Denisons who settled in America in the colony times.