The company began in 1850 when Samuel Merrill bought an Indianapolis bookstore and entered the publishing business. After his death in 1855, his son, Samuel Merrill, Jr. continued the business. Soon after the Civil War the business became Merrill, Meigs, and Company, and in 1883 the name changed again to the Bowen-Merrill Company. In 1903 the name became the Bobbs-Merrill Company, after long-time director, William Conrad Bobbs. From 1899 through 1909, the company published 16 novels whose sales placed each of them among the nation's top ten best-selling books of the year for one or more years.
Bobbs-Merrill was known for publishing such authors as Erving Goffman, Richard Halliburton, David Markson, Ayn Rand, James Whitcomb Riley, Walter Dean Myers, Irma S. Rombauer and Keith Ayling. Of note, Keith Ayling wrote The Story of Old Leatherneck of the Flying Tigers (1945). Bobbs-Merrill also published the early works of fantasy writer L. Frank Baum.
In 1949, Bobbs-Merrill commissioned artist Evelyn Copelman to illustrate a new edition of The Wonderful Wizard of Oz, reprinted as The Wizard of Oz and The New Wizard of Oz. Copelman's illustrations were more influenced by the 1939 Judy Garland MGM film version of the book than by W.W. Denslow's original 1900 illustrations, although the credits on the book stated otherwise.  1949, the year that Copelman's illustrations first appeared, was also the year of the film's first re-release.
Bobbs-Merrill was also responsible for publishing the official records of the State of Indiana and texts in the history of philosophy.
In 1959, The Howard W. Sams Company purchased Bobbs-Merrill. When Sams was acquired by Macmillan in 1985, the Bobbs-Merrill name ceased being used with the exception of continued sales of the Fifth Revision of The Joy of Cooking, which continued to be a steady seller for Macmillan, as well as selected College Division titles such as the Library of Liberal Arts.