I have pieced together all of the officers who served in the 2nd U.S. Cavalry during the Civil War with the help of the regimental monthly returns and annual Army Registers. Readers will quickly note the large number of resignations. The 2nd was the hardest hit of the five cavalry regiments by resignations at the beginning of the war, with 19. Of these, 10 went on to become general officers in the Confederate Army and four others reached the rank of colonel. Nineteen officers who served in the regiment were general officers of either regulars or volunteers in the Union Army by the end of the war. Twenty one of these officers were commissioned from the ranks. Of the field grade officers listed here, only Pleasonton and Whiting actually served in the field with the regiment during the war. Readers will note the scarcity of second lieutenants by the end of the war. The 1865 Army Register shows only one, Patrick Horrigan, and he was promoted to first lieutenant on January 5, 1865.
Colonels
Philip St.G. Cooke promoted to Brigadier General November 12, 1861
Thomas J. Wood
Lieutenant Colonels
Marshall S. Howe transferred Colonel 3rd U.S. Cavalry
Enoch Steen retired September 23, 1863
Innis N. Palmer
Majors
Charles A. May resigned April 20, 1861
Lawrence P. Graham transferred Lieutenant Colonel 5th U.S. Cavalry
William N. Grier transferred Lieutenant Colonel 1st U.S. Cavalry
Washington I. Newton retired October 26, 1861
John W. T. Gardiner retired November 14, 1861
J. W. Davidson
Alfred Pleasonton
Charles J. Whiting dismissed November 5, 1863
Frank Wheaton
Captains
Henry H. Sibley resigned May 13, 1861
Reuben P. Campbell resigned May 11, 1861
William Steele resigned May 31, 1861
Richard H. Anderson resigned March 3, 1861
James M Hawes resigned May 9, 1861
William D. Smith resigned January 28, 1861
Samuel H. Starr transferred Major 6th U.S. Cavalry
John Buford transferred Army Staff
Charles H. Tyler dismissed June 6, 1861
Beverly Robertson dismissed August 8, 1861
Jonas P. Holliday KIA April 5, 1862 (as Colonel 1st Vermont Cavalry)
Charles E. Norris
Thomas Hight resigned April 27, 1863 (later Colonel, 31st Maine Infantry)
George A. Gordon
Francis N.C. Armstrong resigned August 13, 1861
Henry Brockholst Livingston retired August 25, 1862
John Green
Lewis Merrill
John K. Mizner
Charles J. Walker
Wesley Merritt
Theophilus F. Rodenbough
Charles W. Canfield KIA June 9, 1863
Robert E. Clary dismissed February 13, 1864
David S. Gordon
Robert S. Smith resigned January 25, 1865
Charles McK. Leoser
James F. McQuesten KIA September 19, 1864
George O. Sokalski
Henry E. Noyes
First Lieutenants
George B. Anderson resigned April 25, 1861
John Pegram resigned May 10, 1861
John B. Villepigue resigned March 31, 1861
John Mullins resigned April 24, 1861
Ebenezar Gay transferred to Captain, 16th U.S. Infantry
George Jackson resigned June 1, 1861
William P. Sanders transferred to Captain, 6th U.S. Cavalry
Charles H. Gibson resigned May 30, 1864
Edward Ball
James W. Duke died October 28, 1862
Thomas W. Burton dismissed October 24, 1862
William Blanchard
John Mix
Thomas B. Dewees
William H. Harrison
Lewis Thompson
Frederick W. Schaurte
James G. Potter resigned April 27, 1863
Frank Burnham dismissed November 25, 1863
Robert Lennox
Michael Lawless KIA June 11, 1864
Edward J. Spaulding
Elijah R. Wells
Paul Quirk retired January 5, 1865
Charles H. Lester
James Cahill
Charles McMaster KIA October 25, 1864
James Egan
Patrick W. Horrigan
Second Lieutenants
Thomas J. Berry resigned January 28, 1861
Solomon Williams resigned May 3, 1861
James C. Snodgrass resigned June 13, 1861
Francis H. Parker transferred to 3rd U.S. Artillery, then Ordnance Corps
Edwin M. Coates transferred to 12th U.S. Infantry
Peter Rinner cashiered February 13, 1864
Charles Lewis dismissed June 3, 1864
Daniel Flynn retired September 30, 1863
Theodore M. Spencer dismissed December 5, 1863
George DeVere Selden died September 17, 1863
Stephen DeW. C. Beekman died July 7, 1864
Resources:
Cullum, George W. Biographical Register of the Officers and Graduates of the U.S. Military Academy, Volume 2. Boston: Houghton, Mifflin and Company, 1891.
Heitman, Francis B. Historical Register and Dictionary of the United States Army. Washington: Government Printing Office, 1903.
Henry, Guy V. Military Record of Civilian Appointments in the United States Army, 2 volumes. New York: George W. Carleton, 1869.
National Archives, Record Group 94, U.S. Returns from Regular Army Non-infantry Regiments, 1821-1916: 2nd U.S. Cavalry
Rodenbough, Theophilus F. From Everglade to Canyon with the Second United States Cavalry. Norman: University of Oklahoma Press, 2000.
U.S. Army Registers, 1861-1865
Warner, Ezra J. Generals in Blue. Baton Rouge: Louisiana State University Press, 1964.
Warner, Ezra J. Generals in Gray. Baton Rouge: Louisiana State University Press, 1959.
Regular Cavalry in the Civil War 
you missed Eugene M. Baker, Captain at that time. USMA 1859.
John, that’s incorrect. While Baker was assigned to the regiment as a brevet second lieutenant in 1859, he was assigned to the 1st Dragoons the following year as a second lieutenant. He spent the intervening time at the Cavalry Practice School at Carlisle, not serving with either regiment in the field. He spent the Civil War with the 1st Dragoons/ 1st Cavalry and didn’t return to the 2nd Cavalry until 1869 as a major. (Heitman, page 102, Rodenbough, From Everglade to Canyon, page 448)