Baldwin County was established on December 21, 1809, ten years before Alabama became a state. Previously, the county had been a part of the Mississippi Territory until 1817, when the area was included in the separate Alabama Territory. Statehood was gained by Alabama in 1819.
There have been numerous border changes to the county and numerous armies have invaded.
In the first days of Baldwin County, the town of McIntosh Bluff on the Tombigbee River was the county seat. (It is now included in Washington County, west of Baldwin County.) The county seat was transferred to the town of Blakeley in 1810, and then to the city of Daphne in 1868. In 1900, by an act of the legislature of Alabama, the county seat was authorized for relocation to the city of Bay Minette, however, the city of Daphne resisted relocation.
To relocate the county seat to Bay Minette, the men of the town devised a scheme. To lure the Sheriff and his deputy out of the Daphne, the men fabricated a murder. While the law was chasing down the fictitious killer during the late hours, the group of Bay Minette men stealthily traveled the seventeen miles (27 km) to Daphne, stole the Baldwin County Courthouse records, and delivered them to the city of Bay Minette, where Baldwin County’s county seat remains. A New Deal mural, completed by WPA artists during the Great Depression, depicts the events. It hangs in the Bay Minette post office .
Due to its proximity to the Gulf of Mexico, Baldwin County frequently endures tropical weather systems, including hurricanes. In recent years, the county was declared a disaster area in September 1979 due to damage from Hurricane Frederic, in July 1997 due to Hurricane Danny, in September 1998 from Hurricane Georges, in September 2004 due to damage from Hurricane Ivan, and again in August 2005 due to damage from Hurricane Katrina.