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William Wheeler enrolled on May 11, 1861 at New York City for one month at the age of 25. He was mustered into Company I, 7th Militia as a Private on May 13, 1861. He was promoted to Sergeant on May 17 and mustered out with the company on June 3.

Wheeler then enrolled at New York City on October 15, 1861 to serve for three years. He was mustered into the Thirteenth Independent Battery as a First Lieutenant that same day. He was commissioned in that grade on May 30, 1862, retroactive October 15, 1861. On August 12, 1863, he was promoted to Captain with rank from May 26 and took command of the Thirteenth, following the resignation of Capt Dieckmann.

William Wheeler was killed in action near Marietta, Georgia on June 22, 1864.