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The Thomas Flournoy papers consist of letters, documents, and receipts of Flournoy, a lawyer from Augusta, Georgia, who commanded in the South during the War of 1812. He served as commissioner to the Creek Indians between 1820 and 1836. The collection consists of over 90 letters, around 20 documents, six receipts, and a lock of hair.

The Correspondence series contains around 25 items relating to Flournoy's military and War of 1812 service, including letters, returns, requisitions, reports, orders, and petitions. They cover a range of topics, such as desertions, courts martials, supplies, and appointments. Approximately 20 letters relate to his position as United States commissioner to the Creek Indians (1820).

• Around ten letters pertinent to legal disputes between Flournoy and Judge George Walton, and the resulting duel between Flournoy and the judge's nephew John Carter Walton (1799-1804).
• This series also incorporates around 20 family letters, including three from his nephew Matthew Wells (November 12, 1806, May 12, 1816, and May 4, 1837), one letter and one letter fragment from his brother John James Flournoy, 15 from his brother Matthew Flournoy, and one reply to Matthew his brother. These discuss business, professional favors, death of a son in Fayette, Kentucky, and family news.
• Letter by Thomas H. Cushing to Thomas Flournoy, on receipt of Flournoy's acceptance of the appointment as Brigadier General (July 17, 1812).
• Letter by Col. Jno. Pray to Thomas Flournoy, giving him an evaluation of conditions, strategic issues, and risks at Savannah, Georgia, referencing African Americans (November 3, 1812).
• Draft letter by Thomas Flournoy respecting the removal of Lt. Col. Houston of the 8th Regiment Infantry (commanding at Savannah) as a result of "mental derangement, which disqualifies him for command." Suspended until further order (November 16, 1812).
• Four official letters between Flournoy and Patrick Jack, colonel of the 8th Regiment of U.S. Infantry (1812).
• A letter from William Harris Crawford, the U.S. minister to France, concerning the management and politics of the war (November 30, 1812).
• A letter from John Houstoun McIntosh, director of the Territory of East Florida, concerning the settlers of Talbot Island and Nassau River, East Florida (December 26, 1812).
• An inspection return from the 3rd Regiment of Georgia militia at Point Peter Battery, Florida [January 9, 1813].
• A copy of Brigadier General Ferdinand Leigh Claiborne's "Talk to the Choctaw Indians" (August 2, 1813).
• A letter from Choctaw Chief Pushmataha (Pooshemataha), signed with his mark, to James Wilkinson, discussing murdered and imprisoned Choctaw Indians (August 9, 1813).
• Three letters between Flournoy and Former South Carolina Governor and Creek Indian negotiator Andrew Pickins, Jr., concerning treaties with the Creek Indians (August 21, 28, and October 30, 1820).
• Three items to and from John C. Calhoun of the War Department.
• Letter from William H. Crawford to Thomas Flournoy, on Georgia and Kentucky politics. "The present governor admits of nothing like neutrality. Whoever is not devoted to him is considered his enemy." (October 2, 1820).
• Nine letters with David Brydie Mitchell, including a communication from Tustunnuggee Thlocco (Tiger Tail) and Tustunnuggee Hopoie (November 10, 1820).
• A letter to John Clarke of Augusta, Georgia, concerning claims of Georgia residents for Creek lands (October 4, 1820).
• An eight page letter from Thomas Flournoy to Rev. Dr. Davies pertains to Flournoy's responses to a sermon sent by Davies. He noted that he asked Judge Longstreet questions about scripture, naming 1 Corinthians 15 in particular, and that Longstreet apparently discussed it in church. An indirect source told Flournoy that he "asked a number of Infidel questions of Longstreet, which he refused to answer" (April 27, 1840).
• A letter from Flournoy's nephew, Thomas C. Flournoy, includes content on Kentucky land business and politics. He praised the oratory skills of Senator Corwin of Ohio (May 17, 1849).

The Documents series (20 items) consists of a list of rules for the duel between Flournoy and Walton (1804); general orders appointing Thomas Flournoy as aide de camp to the Commander in Chief, with rank of Lieutenant Colonel (April 6, 1804); reports on the arms, ammunition, and crew of the gun vessels at the Georgia Station (1813); weekly reports and morning reports of the troops stationed at Fort St. Philip, Fort St. Charles, New Orleans, and for the 2nd Regiment of Light Dragoons; orders from the Southern Department; a transaction record at the Bank of Augusta; and a memo listing "Order of Correspondence relating to the Treaty with the Creek Indians" (1820); and the last will and testament of Thomas Flournoy (July 20, 1856).

The Receipts series (6 items) is comprised of receipts deposited in the Bank of Augusta, Georgia; 2 payments made to John Campbell; and 2 receipts for sugar and brandy.

The papers also include a lock of Thomas Flournoy's Hair, clipped when he was 46 years old.