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Between the Miami council house and the county courthouse, the place was governed from a succession of forts, and its governors were commandants. The French built the first palisaded Fort Miami (Fort St. Philippe des Miamis) at Kekionga — Jean Baptiste Bissot, Sieur de Vincennes, had established a trading post there about 1706, and the fortified post was completed in 1722 under Captain Dubuisson, authorized by Governor Vaudreuil of Canada to hold the trade route against the British. Its garrison ran to twenty or thirty men. The commandants in succession, as Griswold compiled them in his Pictorial History of Fort Wayne, were: Jean Baptiste Bissot, Sieur de Vincennes (1697 in Griswold's dating of his command); François Margane, Sieur de Vincennes (1725); Ensign Douville (1734); Ensign Dubuisson; and Captain Charles de Raimond (1748). In 1747, with Douville and most of the garrison away at Detroit, Huron warriors allied to the British under the chief Nicholas sacked and burned the fort; Dubuisson retook the site with Miami help, and Raimond, judging the old St. Marys site indefensible, abandoned it in 1750 and built the last French fort on the St. Joseph River, near the present junction of St. Joe Boulevard and Delaware Avenue. Neyon de Villiers took command in 1751.
In November 1760, at the close of the French and Indian War, the French garrison formally surrendered Fort Miami to a British ensign named Robert Holmes. Holmes's command ended in June 1763, during Pontiac's War, when he was lured outside the fort and shot by Miami warriors waiting for him; the small garrison was captured and the post passed out of British hands. For the next three decades Kekionga had no permanent garrison at all — British trade flowed through Detroit, and the Miami governed themselves — until the American army arrived in 1794.
The United States built three successive log stockades named Fort Wayne between 1794 and 1819. Their commandants, compiled from the Wikipedia roster of the fort's commanders, the Ball State University "Forts of Fort Wayne" project, and the garrison orderly books printed in Griswold's Fort Wayne: Gateway of the West, 1802–1813, were:
| Commandant | Tenure | Notes |
|---|---|---|
| Lt. Col. Jean François Hamtramck | Oct 1794 – 1796 | Built and first commanded Anthony Wayne's fort; appointed commandant by Wayne's letter of 21–22 October 1794. Transferred to Detroit. |
| Col. David Strong | 1796 – 1797 | Legion veteran; followed Hamtramck, then was transferred north after a poor inspection by Gen. Wilkinson. |
| Col. Jean François Hamtramck | 1797 – 1798 | Second tenure. His son John Francis Hamtramck was born at the fort in 1798 and is sometimes counted the first United States citizen born in Fort Wayne. |
| Col. Thomas Hunt | from 16 May 1798 | A Lexington, Concord and Bunker Hill veteran who had served under Wayne. |
| Capt. Thomas Pasteur | Jul 1802 – Jul 1803 | His garrison orderly book (July 1802–July 1803) opens Griswold's printed garrison records. |
| Maj. Zebulon Pike (the elder) | Jul 1803 – Jan 1807 | The post's orderly books for these years run in Pike's name; Capt. John Whipple also held the command of the post in this span, from late September 1803, in the Ball State project's reconstruction. |
| Capt. Nathan Heald | Feb 1807 – 16 May 1810 | Left Fort Wayne for Fort Dearborn (Chicago), where he commanded during its 1812 evacuation. |
| Capt. James Rhea | 20 May 1810 – 22 Nov 1812 | Commander during the Siege of Fort Wayne, 5–12 September 1812; during the siege his lieutenants relieved him and Lt. Ostrander took command until Gen. William Henry Harrison's army broke the siege on 12 September. Rhea was formally relieved that November. |
| Capt. Hugh Moore | 23 Nov 1812 – 26 Aug 1813 | Per the orderly books printed by Griswold. |
| Maj. John Whistler | May 1814 – Mar 1817 | Built the third Fort Wayne in 1815–16; earlier the builder and first commandant of Fort Dearborn. Lt. Daniel Curtis acted in command from Whistler's transfer to St. Louis in March 1817 until Vose arrived in June. |
| Maj. Josiah N. Vose | Jun 1817 – 19 Apr 1819 | Last commandant. The garrison abandoned Fort Wayne on 19 April 1819 and its stores were shipped to Fort Detroit. |
No commandant for the months between Moore's departure in August 1813 and Whistler's arrival in May 1814 is firmly named in the sources used for this section; the interim command is an open item in the notes to this expansion.