Clone Commandos, also known as Republic Commandos and later as Imperial Commandos, were elite clone troopers of the Grand Army of the Republic and later the Stormtrooper Corps. Cloned from the genetic template of the famous Mandalorian bounty hunter Jango Fett, clones selected for the commando program were trained by Mandalorian drill sergeants that were recruited by Fett himself to train them to become the deadliest soldiers in the Clone Army. Often working in Squads of four, clone commandos were assigned to carry out special operations that the average clone trooper couldn't handle. These missions included covert infiltration, sabotage, demolition and assassination, all of which were standard tasks for the clone commandos.

Delta Squad, with its members being known as the Deltas, was a military special forces squad of the Grand Army of the Republic during the Clone Wars, a galactic civil war between the Galactic Republic and the Confederacy of Independent Systems. The squad consisted of four clone commandos— Clone Sergeant RC-1138, second-in-command RC-1140, RC-1262, and RC-1207— who, on one occasion retrieved the bodies of Jedi Master Halsey and Padawan Knox following the massacre on Devaron and participated in other dangerous missions during the war.

Omega Squad was an elite clone commando unit, and was part of the Grand Army of the Republic during the Clone Wars. The members of this unit were brought together after each of their respective squads were killed during action at Geonosis. Unlike most other commando squads, the Omegas wore specialized Night Ops Armor. It was part of Arca Company of Zero Five Commando.

Yayax Squad was an elite clone commando unit, and was part of the Grand Army of the Republic during the Clone Wars. They were one of the squads trained by Rav Bralor on Kamino. Members of Yayax Squad, like those of Omega Squad, wore matching Katarn armor, a gray-and-brown dazzle-pattern which gave them a degree of camouflage in an urban environment. This gave them an advantage during the Battle of Coruscant.

Clone Force 99, unofficially known as the "Bad Batch," was a clone commando special forces squad that was active during the Clone Wars. The squad initially consisted of four clone commandos that were designed with genetic mutations and led by Clone Sergeant "Hunter," a clone with enhanced sensory abilities. Other members of the squad included CT-9904 "Crosshair," a clone with keen eyesight and marksmanship that allowed him to excel in long distance firefights, "Wrecker," a reckless clone with enhanced muscular form, and "Tech," a clone with enhanced mental capacity and intelligence. Following the crucial Battle of Anaxes, Advanced Recon Commando Clone Corporal CT-1409 "Echo" joined the unit.