Officer manning within the Regular regiments started the war below full strength and never recovered. At the beginning of 1861 the Regular Army had only 16,367 of its authorized strength of 18,093 officers and men, and there had been no increase in strength since 1855 (Sawicki, Cavalry Regiments of the U.S. Army, pg 46). These numbers quickly dwindled as southern born (and some northern born) officers resigned their commissions and left the army.
As mentioned previously, four of the five commanders of the mounted regiments resigned. Many are aware that the one who did not, Philip St. George Cooke of the 2nd Dragoons, was a Virginian. The other officer ranks fared little better. Of the officers assigned to the 2nd Dragoons on January 1, 1861, 1 of 2 majors resigned, 6 of 12 captains resigned and 2 more retired. Seven of the twelve first lieutenants resigned or deserted. One of these, Francis N.C. Armstrong, resigned after leading his Company K for the Union during the first battle of Bull Run (Rodenbough, From Everglade to Canyon, pg 462). Those who remained were promoted and distributed among all five regiments.
Unlike the seemingly limitless number of volunteer regiments organized during the war, there were a finite number of Regular regiments, and officer billets within them. Total numbers included six colonels, six lieutenant colonels, eighteen majors, and 72 captains. Officers were commissioned and assigned against a specific billet in a specific regiment. These were the only billets authorized by Congress, and there were not any spares. Assignments outside the regiments for such things as instructors at the Cavalry School at Carlisle Barracks or aides de camp to general officers were taken out of hide from the regiments. If you were the regimental commander and one of your captains was teaching at West Point, for example, you did without a captain and a first lieutenant commanded one of your companies. Once assigned to a regiment as a second lieutenant, one remained a second lieutenant until a billet was vacated by one of the first lieutenants, via promotion, resignation, or death. It was possible, however, to be promoted to another regiment.
Even promotions worked against the strength of the Regulars, due to the promotion system of the Regular Army. During the course of the war, it was not uncommon for regular officers to take leaves of absence to lead volunteer units. These officers did not resign, and continued to count against the assigned strength of the regiment. Alfred Pleasonton, for example, occupied a major’s billet in the 2nd for the entire Civil War, even while commanding the Cavalry Corps of the Army of the Potomac. At the end of the war, Wesley Merritt was likewise still assigned to the regiment, one of five major generals of volunteers on the rolls (Rodenbough, 371).
Senior officers within the regiments were rarely present with them. Thomas J. Wood, who succeeded Cooke in command of the 2nd when he was promoted to Brigadier General in November 1861, was commanding a brigade and then a division in the Tennessee and Mississippi campaigns. He remained in the western theater throughout the war, and never served with the regiment that he nominally commanded (Rodenbough, pg 438). This is one of the reasons that captains are usually noted as leading Regular regiments in reports in the Official Records and elsewhere. Indeed, this problem did not go away after the war. Regimental returns from November 1, 1866 show seven generals of volunteers assigned to the 2nd Cavalry, with a captain actually present commanding the unit and lieutenants commanding seven of the twelve companies (Rodenbough, pg 371).
New officers did join the regiments as the war progressed. Eleven new lieutenants joined the 2nd in 1861, four of them newly commissioned West Point graduates. Never, however, were they at a full complement of officers. The only possible exception to this might be the 6th US Cavalry, since it formed in the summer of 1861. Given the very active service of this regiment throughout the war, however, it is doubtful that they stayed at strength for long.