Confusion was caused by the commanders not being able to distinguish their Confederate troops from the Union troops. The Confederate "Stars and Bars" were too easily confused in the smoke of battle with the Union "Stars and Stripes", resulting in very real military mistakes.

To remedy this, Gen. P.G.T. Beauregard, of the Army of Virginia, and others sought a better design. He attempted to have the Confederate flag changed but Congressman William Porcher Miles suggested that the army adopt its own distinctive battle flag, and recommended the design he had presented to the Congress as the Confederate Flag on March 4, 1861. This flag was agreed upon, but it was recommended that it would be more convenient and lighter as well as less likely to be tore by bayonets or tree branches if made square. This flag proved so popular, that it became basis for the Second National flag of the Confederacy. Some prefer the square proportions of this flag over Mile's original rectangle as more sonorous and more distinct — and therefore a better symbol of the South. It was used in battle from November 1861 to the fall of the Confederacy.

The battle flag of the Confederacy is square, of various sizes for the different branches of the service: 48 inches square for the infantry, 36 inches for the artillery, and 30 inches for the cavalry. Other flags, such as State regimental colors, were used by the Confederacy on the battlefield, but the Battle Flag, although it was never officially recognized by the Confederate government, came to represent the Southern "cause" to most people.

The first recorded use of the lone star flag dates to 1810. On September 11, 1810 a troop of West Florida dragoons set out for the provincial capitol at Baton Rouge under this flag. They were joined by other republican forces and captured Baton Rouge, imprisoned the Governor and on September 23, 1810, raised their Bonnie Blue flag over the Fort of Baton Rouge. Three days later the president of the West Florida Convention, signed a Declaration of Independence and the flag became the emblem of a new republic. By December 10, the flag of the United States replaced the Bonnie Blue after President Madison issued a proclamation declaring West Florida under the jurisdiction of the Governor of the Louisiana Territory.

With this rebellion in mind, this flag was used by the Republic of Texas from 1836 to 1839. On January 9, 1861 the convention of the People of Mississippi adopted an Ordinance of Secession. With this announcement the Bonnie Blue flag was raised over the capitol building in Jackson. Harry McCarthy was so inspired that he wrote a song entitled "The Bonnie Blue Flag" which became the second most popular patriotic song of the Confederacy.

The Confederate government did not adopt this flag but the people did and the lone star flags were adopted in some form in five of the southern States that adopted new flags in 1861.

The "Jack" was the flag of the Confederate Navy. This flag was used mainly by the Confederate Navy but also by some ground troops.

The Confederate Navy Jack, also called "The Southern Cross," is rectangular, usually about 5×3 feet. The blue color in the saltire (the diagonal cross) is much lighter than in the Battle Flag, and it was flown only on Confederate ships from 1863-1865. This flag is what is typically recognized as the Confederate flag, but this is not strictly accurate.

The design was originally made by South Carolina Congressman William Porcher Miles to be the 1st National Flag, but it was rejected by the Confederate government for looking too much like crossed suspenders. It was used by a few army units, including the Army of Tennessee, as their battle flag.

Today, it is the most universally recognized symbol of the South, where it is commonly called the Rebel or Dixie flag. The Southern states or The South, was known during the Civil War era as "Dixie".

This flag was adopted but never officially enacted. For 25 days, the Confederate States of America had no officially approved flag. In their haste to have a flag prepared for the flag raising ceremony on March 4, 1861, Congress neglected to formally enact a flag law. When this flag was first raised over the capitol building in Montgomery, it contained 7 stars, representing the Confederate States. By the third week of May, 2 more stars were added representing Virginia and Arkansas. In July, the addition of North Carolina and Tennessee increased the number to 11 and finally the admission of Kentucky and Missouri in December brought the circle of stars to 13.

During battle, this flag was sometimes confused with the Union Stars and Stripes, therefore it was replaced by the 2nd National flag in 1863.

This flag was flown from March 5, 1861 to May 1863 as the first official flag.

Not more then a year after the adoption of the "Stars and Bars", the issue of designing a new flag for the Confederate States was raised with the intention to create a flag that was in no way similar to the Union's "Stars and Stripes". To avoid confusion, the new Battle Flag was placed in the top, left quarter of the flag. When the battlefield was windless, it was mistaken for a surrender flag because all that could be seen was the field of white. Stainless Banner flag of the Confederate States of America. ... May 1 is the 121st day of the year in the Gregorian calendar (122nd in leap years). ... 1863 is a common year starting on Thursday.

Adopted on May 1, 1863, this flag displayed the Battle Flag in the canton on a field of pure white, giving it it's name the "Stainless Banner", to refer to "the unspotted virtue and honor of Southerners and their fight for independence from the tyranny and aggression of northern states."

One of the first uses for this flag was to drape the coffin of Gen. Thomas J. "Stonewall" Jackson. Jackson died on May 10, 1863 from a case of pneumonia that he contracted in the treatment of his injuries received at the Battle of Chancellorsville on May 2nd.

On the 12th, his body lay in state in the Confederate House of Representatives, by order of the President Jefferson Davis, the first new flag manufactured draped his coffin. The flag is often referred to as the "'Stonewall' Jackson Flag".

This "Stainless Banner" is now on display in the Museum of the Confederacy in Richmond, Virginia.

Due to the fact that the 2nd National's pure white field could be mistaken for a flag of surrender, on March 4, 1865 this last flag of the Confederacy was adopted.

This design added a red bar to the end of the "Stainless" flag. The red vertical stripe was added to dispel confusion with the flag of surrender when the flag was not unfurled. This flag flew for 36 days in 1865 until the South surrendered on April 9th. The flag was also known as "Stainless".