The American Naturalist, a peer-reviewed publication about ecology, evolution, and population and integrative biology research was established in 1867, by Alpheus S. Packard Jr. (1839-1905), Frederick W. Putnam, Edward S. Morse, and Alpheus Hyatt. All of them had been students of Louis Agassiz, and assistants at the Harvard University's Peabody Museum. When the Peabody Museum tried to prevent the four men from working on their own research after hours, they went to the Essex Institute and Peabody Academy of Science in Salem, Massachusetts. The first issue of The American Naturalist was published in March 1867, as "A Popular Illustrated Magazine of Natural History". In 1878, Packard, Putnam, Morse, and Hyatt turned the journal over to Packard and Edward Drinker Cope. Packard and Cope managed the journal until Cope's death in 1897, at which time it was taken over by a group of men from the Peabody Museum, Harvard University, and Tufts.

The journal became the official publication of the newly formed Society of Naturalists of the Eastern United States (later the American Society of Naturalists), in 1885 . In 1907, the journal was sold to J. McKeen Cattell, who acted as editor and publisher until his death, after which his roll passed to his heirs. In 1908, the journal's focus switched to "... Advancement of the Biological Sciences with Special Reference to the Factors of Evolution." In 1951, American Society of Naturalists assumed editorial control of the journal. In 1967, Cattell's heirs decided to leave publishing, and the journal was purchased by the University of Chicago Press (American Society of Naturalists).