Hernando de Soto was a Spanish conquistador who landed in present-day Florida in 1539, then led an expedition exploring the southeastern and midwestern parts of North America carrying this flag.

In 1663 King Charles II´s land grant established Carolina whose westward border was then considered the Mississippi River. Therefore, technically this flag held dominion over that vast territory which included Mississippi. In reality, the western area was not explored or populated by the British during this period, and most likely this flag probably never actually flew over Mississippi.

The French explorers Cavelier and La Salle claimed the Mississippi Valley in 1682, naming it Louisiana in honor of King Louis XIV. In 1699 Sieur d'Iberville established the first permanent settlement in Mississippi near present-day Ocean Springs.

At the end of the worldwide struggle of the Seven Years War, fought between the French and English and their allies, the dominion over Mississippi once again passed to the English. What had started in the Ohio River Valley as the French and Indian War, now resulted in new colors (the British Red Ensign that had been adopted by Queen Anne in 1707) being raised at Natchez, Baton Rouge, Mobile, and Pensacola in 1763.

Under the provisions of the Treaty of Paris of 1763, France ceded its territory east of the Mississippi River to England, and its territory west of the river, along with New Orleans, to Spain. Manuel Gayoso would served as the first Spanish governor, first at Fort Natchez, and later in New Orleans.

The French indirectly once again controlled Mississippi in 1800, through its ally Spain, in reality a puppet of the French Empire. Napoleon Bonaparte had gained Louisiana from Spain under the secret Third Treaty of San Ildefonso. Louisiana remained nominally under Spanish control until a transfer of power to France on November 30, 1803, just three weeks before the cession to the United States.

Parts of Mississippi were first organized as a territory of the United States in 1798 from land that was disputed by the United States and Spain, even before the Louisiana Purchase of 1803. The Territory of Mississippi was an organized incorporated territory of the United States that existed from 1798 until 1817, when the final extent of the territory was admitted to the Union as the state of Mississippi. This area extended from 31º N latitude to 32º28' North, or approximately the southern half of the present states of Alabama and Mississippi. The Mississippi Territory was expanded in 1804 and again in 1812 until it extended from the Gulf of Mexico to the southern border of Tennessee.

When Mississippi joined the Union as the 20th state in 1817, because there was no provision for how the stars should be arranged, this unusual circular union was one used on this rare Mississippi national stars and stripes. This flag represents one of only four known surviving 20 star flags. It is currently in the collection of the Museum Division, Mississippi Department of Archives and History, and undergoing restoration.

The United States claimed West Florida as part of the Louisiana Purchase of 1803, but the claim was disputed by Spain. Spain claimed that West Florida was a part of its Florida colony, not part of Louisiana. While the United States and Spain negotiated on the status of West Florida, American settlers led a rebellion in 1810 and establishment the independent Republic of West Florida, with its capital located at St. Francisville on a bluff overlooking the Mississippi River in present-day Louisiana. The Bonnie Blue flag flew over the territory briefly for 74 days.

During the Civil War there were basically three national flags for the Confederacy. The first two saw use in Mississippi, and possibly the third, although not documented.

This battle flag was used by Mississippi troops when under the command of General P.G.T. Beauregard, who apparently designed the original. It later was made the canton of Mississippi State flag. There were both non-fimbriated and fimbriated versions of the flag being used.

The State of Mississippi was also briefly called the "Sovereign Republic of Mississippi" prior to the formation of the CSA, and used "...a Flag of white ground, a Magnolia tree in the centre, a blue field in the upper left hand corner with a white star in the centre, the Flag to be finished with a red border and a red fringe at the extremity of the Flag."

This variant flag design was most likely a post war flag. It was used by one or more Mississippi United Confederate Veterans units, and over time became mistakenly identified as the original Magnolia flag.

The flag illustrated here is only one variant of the Mississippi State flag that existed between 1894 and 1995. During this period, the dimensions of the Southern Cross, the size of the stars, and their orientation were not standardized. There were literally dozens of variants of the Mississippi flag. There were both non-fimbriated cantoned versions and the fimbriated cantoned versions of the flag being used interchangeably by the state government until 1995.

The Mississippi Flag was standardized in 1995 at the request of the governor who noticed that different flag variants were being flown on government buildings. Until then there were no specifications for the Mississippi State flag as to where the stars should be placed, what their size should be, what direction they should point or if the canton should be fimbriated. In 1995, Governor Kirk Fordice sent an official memorandum, largely based on the work of Mississippi vexillologist Clay Moss, to every manufacturer and officially standardized the format of the canton.

In 2001 a flag referendum was declared offering this flag as an alternative to the standardized flag of 1995. It basically replaced the controversial Southern Cross with a star pattern. It had a blue canton with 20 stars. The outer ring of 13 stars represent the original 13 colonies. The next ring had six stars representing the six nations that historically had sovereignty over the Mississippi territory prior to statehood. These were Native Americans, the French, the Spanish, the British, and the United States and the Confederate States. The inner and slightly larger star represented Mississippi itself, and the 20 stars also indicated that Mississippi was the 20th state.

As the State of Mississippi continued to wrestle with a decision to replace its existing state flag with its controversial Confederate battle flag in the canton, a sudden decision in 2019 came from its legislature to once again to replace the existing flag. It generated field of about 3,000 public submissions, with the only requirement being it had to contain the text "In God We Trust" somewhere in its design.