During the Clone Wars, the clone trooper captain was a specialized clone trooper breed which was bred on Kamino as battlefield officers and special mission operatives.
Rex, Captain of the 501st Legion, in his customized Phase II armor
At the start of the war, clone trooper captains were recognized by their unique red markings on their helmets and torso armor, but as the war progressed, clone trooper armor became more customized, and red markings no longer signified the rank of captain. Clone trooper captains were assigned to lead companies of 144 standard clone troopers, which were divided into four separate platoons. Each platoon was commanded by a clone trooper lieutenant who would report directly to their respective captains. These clones were often equipped with a DC-15A blaster rifle and a line of thermal detonators, although as the war progressed a number of clone captains would use specialized weaponry which suited their respective combat styles. Trained in both squad- and company-level tactics, as well as to handle the 74-Z speeder bike, clone trooper captains were diverse leaders.
Clone trooper captains first appeared during the First Battle of Geonosis wearing Phase I armor. The officers commanded at Forward Command Centers and positions of great visual range. A handful of captains used speeder bikes to destroy the huge and clumsy Confederacy OG-9 homing spider droids, throwing pulse grenades as they raced across the battlefield. Also, a branch of jet trooper captains participated in many prominent battles, such as Mace Windu's defense of Dantooine. Some time after first battle on Geonosis, clones began customizing their armor in various color schemes and patters. This carried on into the use of Phase II armor. One notable clone captain was Rex, who fought on the front lines with the grit of an Advanced Recon Commando. He participated in many campaigns throughout the war and was initially the senior clone officer of the elite 501st Legion until clone trooper sergeant Appo was promoted and became a clone trooper commander, taking over Rex's duties as the legion's commanding officer.