Morgan, the county seat of Calhoun County, was incorporated May 5, 1856. The county was designated from parts of Baker and Early Counties. The county is named for John C. Calhoun of South Carolina, who served as Vice President of the United States in 1832. The city is said to be named for General Daniel Morgan, a Revolutionary War figure.

Morgan is not the principle city in Calhoun County. The cities of Edison and Arlington are larger. However, the county seat is located in Morgan as it is centrally located in Calhoun County.