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The Confederate States Bureau of Indian Affairs was a subdivision of the Confederate States War Department established in 1861 to handle the duties the War Department was charged with regarding the Confederacy's relations with the various Indian Nations with which it interacted.
| Image | Name | Took office | Left office |
|---|---|---|---|
 | David Hubbard | 15 March 1861 | 7 April 1862 |
| Sutton S. Scott | 8 April 1862 | 1863 | |
| | David Hubbard | 1863 | 21 February 1865 |
 | Brig. Gen. Douglas H. Cooper | 21 February 1865 | April 1865 |
| Image | Name | Took office | Left office |
|---|---|---|---|
 | Brig. Gen. Albert Pike | 16 March 1861 | ? 1862 |
 | Brig. Gen. Benjamin McCulloch | ? | 7 March 1862 |
| | Brig. Gen. Albert Pike | 7 March 1862 | 5 November 1862 |
| | Col. Douglas H. Cooper | 5 November 1862 | 8 January 1863 |
 | Brig. Gen. William Steele | 8 January 1863 | 11 December 1863 |
 | Brig. Gen. Samuel B. Maxey | 11 December 1863 | 21 February 1865 |
| | Brig. Gen. Douglas H. Cooper | 21 February 1865 | April 1865 |
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