This flag is an Army of Northern Virginia, 3rd wool bunting issue. Flags of this issue were manufactured at the Richmond Depot between July 1862 and May 1864. The flag of the 59th Alabama Infantry was captured near Hatcher's Run, Virginia, on March 25, 1865, by Private George W. Tompkins, Co. F, 124th New York Infantry.
http://www.mycivilwar.com/regiments/csa-al/al_inf_59_reg.htm
A brigade of North Carolina cavalry from Maj Gen. Fitzhugh Lee's division tried to secure the Namozine Church road intersection until Johnson could return and take the correct fork. About noon, one of Custer's brigades under Col. William Wells attacked the still deploying Confederate cavalry. Custer's younger brother, Thomas, spurred his horse over a hastily thrown up barricade and captured 3 Confederate officers and 11 enlisted men, as well as the battle flag of the 2nd North Carolina Cavalry
http://www.mycivilwar.com/battles/650403a.htm
Federal report, flag captured at Selma, Ala., on April 2, 1865, said by bearer to be flag of 11th Mississippi
http://www.mycivilwar.com/regiments/csa-ms/ms_cav_11_reg.html
The flag was captured on May 22, 1863, near Middleton, Tennessee, by Sergeant Major George W. Clark, Private Lewis H. Wilcox and Private Charles F. Parker, Co. B, 4th Michigan Cavalry. The flag was found in a wagon in which three Confederates were attempting to escape after the camp of the 1st Alabama Cavalry was overrun. The flag was eventually taken to Michigan.
http://www.mycivilwar.com/regiments/csa-al/al_cav_01_reg.htm