Although most closely identified with the Confederate Battle Flag, this can also refer to The Bonnie Blue Flag or any of several other Confederate flags: the Stars and Bars (the first official flag) or two later variants.
The Stars and Bars was too like the Union flag, which led to battlefield confusion. In 1863 the Confederacy adopted a new official flag, the "Stainless Banner", essentially the Battle Flag as the canton¹ on a white field. Majorly dumb idea - the flag was too easily mistaken for a white flag of surrender. By 1865 a red bar was added to the fly end of the flag to prevent this error - this flag was flown by Robert E. Lee's Army of Northern Virginia in the last days before Appomattox.
I hate to dispute you folks who live in The South ... but ... the Stars and Bars is not the same as the Confederate Battle Flag as implied above. See the descriptions of the Stars and Bars and the Confederate Battle Flag.
Note: I will gladly stand corrected if need be ...
1. Webby explains this badly. The top left corner (sometimes top half but left third) of the flag. The blue square where the stars are on the American flag.