Mississippi established its independence through secession on January 9, 1861. When it separated itself, there was still no Confederate States of America. Similar to other states in the southern region, Mississippi stood on its own.
After the separation, the people of Mississippi went back to using an old flag which used to be presented in the old Republic of Florida in 1810. The banner included one white star and a blue field. Because of the blue background, it was referred to as the Blue Bonnie Flag. It was used in a marching song too.
Another name for such banner is the Magnolia Flag, which included one Magnolia tree and a white background. You might also see some versions with a red fringe or bar. The Bonnie Blue picture is also placed on one corner. For 33 years, the Magnolia Flag became the official flag of Mississippi, representing the Confederate States of America.
After some time, people indicated that it was sometimes confusing to distinguish the Bonnie Blue flag from the US national banner. It was hard to point out which flag showed the stars and stripes and which one showed the stars and bars. Also during battle, soldiers would be confused as to which flag was which.
The banner then went through a number of changes to make it more unique and show a difference from the US national flag. the Mississippi flag, although now in a standard size, was supposed to be bigger, with the length twice longer than the width.