Following the successful conclusion of the Mexican–American War, the administration of the United States Army was theoretically directed, under the President of the United States, by the Secretary of War and the general in chief. In practice the Secretary of War and the heads of the army's staff agencies—who reported directly to him (adjutant general, quartermaster general, commissary general, inspector general, paymaster general, surgeon general, chief engineer, colonel of topographical engineers, and colonel of ordnance)—exercised full authority, leaving the general-in-chief a figurehead. With a lack of central direction, policy and strategy were de facto developed by the commanders of the numbered geographical departments and three division headquarters. After October 31, 1853 the division echelon was eliminated and the six western departments consolidated into four (Departments of Texas, New Mexico, the West, and the Pacific), whose department commanders employed their troops as they saw fit. The system returned to six departments in 1858 when the Department of Utah was created in January, and the Department of the Pacific split into the Departments of California and Oregon in September.
Military activity affecting one department often originated in another department, preventing efficient use of limited manpower and coordination of efforts. Friction between the Secretaries of War and the generals in chief, and particularly between Jefferson Davis and Winfield Scott, obstructed reforms in the staff system that might have brought unity of command and civilian control of the military. The expansion of the army during the Civil War saw a proliferation in the numbers of geographic departments and their subordinate districts, often changing names and areas under their individual control, some departments eliminated or renamed, only to be recreated again in altered form.
Departments of the Missouri and Kansas
The Department of Missouri resulted from the reorganization and breakup the Department of the West on November 9, 1861, after Abraham Lincoln fired John C. Frémont when he would not rescind his order emancipating the slaves of Missouri and imposing martial law on the state. David Hunter served briefly as the last commander Department of the West. The new department included Missouri, Arkansas, Illinois, Kentucky west of the Cumberland River and at times, Kansas. It briefly merged with the Department of Mississippi in 1862, but was recreated September 19, now consisting of Missouri, Arkansas, Kansas, and the Indian Territory. Colorado and Nebraska were added on October 11, 1862, and the department became generally known as the Department of the Missouri. From 1862 to 1865 the department was primarily concerned with fighting Confederates in Missouri and Arkansas.
The Department of Kansas was created for a third time on January 1, 1864, removing major areas from the military jurisdiction of the Department of the Missouri. The new commander of the Department of Kansas, Maj. Gen. Samuel R. Curtis, had two districts (Colorado and Nebraska) wholly involved in Indian warfare, but Curtis was absorbed with fighting Confederates in the Indian Territory and bushwackers in Kansas, allowing his other districts, but particularly Colorado, complete autonomy. Governor John Evans and Colorado district commander Col. John M. Chivington took advantage of this lack of oversight to aggressively attack Cheyenne villages in April 1864, igniting a major Indian war in July. Curtis created a new , to wage the war but he was wholly incapable of locating his opponents. In his other District of Nebraska, the warfare was even more intense, but the forces there too weak to deal with it.
- Henry W. Halleck (November 19, 1861 to March 11, 1862)
- Samuel R. Curtis (September 24, 1862 to May 24, 1863)
- John M. Schofield (May 24, 1863 to January 30, 1864)
- William S. Rosecrans (January 30, 1864 to December 9, 1864)
- Grenville M. Dodge (December 9, 1864 to June 27, 1865)
- John Pope (June 27, 1865 to 1866)
- Winfield Scott Hancock (1866–1867)
- Philip Sheridan (1867–1869)
- John Schofield (1869–70)
- John Pope (1870–1883)
- Christopher Columbus Augur (1883–1885)
- Nelson Appleton Miles (1885–1886)
- Thomas Howard Ruger (1886)
- Orlando Bolivar Willcox (1886–1887)
- --- (1887–1891)
Department of Missouri Camps, Forts and Posts
- Bear Creek Redoubt (1870–1878)
- Camp Caldwell (1884–1885)
- Camp Crawford (1868)
- Crisfield Post (1885)
- Camp Drywood (1871)
- Camp Grierson (1866)
- Camp Hoffman (1867)
- Camp Kirwin (1865)
- Camp Ogallah (1867)
- Camp Pliley (1869–1870?)
- Camp Wichita (1868–1869)
- Cimarron Redoubt (1870–1876)
- Fort Aubrey (1865–1866)
- Fort Bissell (1873–1878)
- Fort Dodge (1865–1882)
- or Downer's Station (1867–1868)
- Fort Harker (1866–1872)
- Fort Hays (1865–1889)
- Fort Larned (1859–1878)
- Fort Leavenworth (1827–present)
- Fort Lincoln (1861–1879)
- Fort Lookout (1866–1870s)
- Fort Riley (1853–present)
- Post of Southeastern Kansas (1869–1873)
- Fort Solomon (1864–1865)
- Fort Montgomery (1861–1869)
- Fort Wallace (1865–1882)
- Fort Zarah (1864–1869)
- or Fort Lookout (1866–1868)
- Pond Creek Station (1865–1866)+
- + Army fortified Butterfield Stage stations along the Smoky Hill River route.
Indian Territory and Territory of Oklahoma
- or Fort Beach or Fort Otter or Camp Otter (1874)
- or Camp at Kingfisher (1889)
- (1879–1882, 1885)
- Fort Arbuckle (1851–1870)
- Fort Cobb (1859–1862, 1868–1869)
- Fort Gibson (1824–1901)
- Fort Reno (1875–1948)
- Fort Sill (1869–present)
- Depot on the North Fork Canadian River and Camp Supply (1868–1878)
- Fort Supply (1878–1894)
- Robert W. Frazer, Forts of the West: Military Forts and Presidios, and Posts Commonly Called Forts, West of the Mississippi River to 1898 (Norman: University of Oklahoma Press, 1965).
- Raphael P. Thian, Notes Illustrating the Military Geography of the United States, 1813-1880 (Washington, D.C.: Government Printing Office, 1881; reprinted Austin, TX: University of Texas Press, 1979).
- Francis Paul Prucha, A Guide to the Military Posts of the United States, 1789-1895 (Madison: State Historical Society of Wisconsin, 1964).
- Utley, Robert M. (1967). Frontiersmen in Blue: The United States Army and the Indian, 1848-1865. University of Nebraska Press. ISBN 978-0-8032-9550-6.
- The Civil War Day by Day: An Almanac, 1861–1865, by E.B. Long with Barbara Long, 1985, De Capo Press, ISBN 0-306-80255-4, page 138