He joined the U.S. Army as a private in Company F of the Regiment of Mounted Riflemen on June 19, 1846, and was soon promoted to Sergeant.
On June 28, 1848, he was brevetted as a second lieutenant in the 6th U.S. Infantry and served in the Mexican–American War under Generals Zachary Taylor and Winfield Scott.
With the outbreak of the Civil War, Bootes served in the Regular Army with the combined 1st and 6th U.S. Infantry and was wounded at Antietam and again at Gettysburg, where he led his regiment in fighting near the Wheatfield.
For his gallantry and leadership, he was promoted to Major (United States) of the 17th U.S. Infantry in October 1863, a position he held through the remainder of the war.
Shortly thereafter, on January 1, 1871, he received his final assignment, serving as lieutenant colonel of the 25th U.S. Infantry until his retirement from active service in October 1874.