Flags were tools used by many different factions to increase their influence over a certain location. The Assassins were notorious for removing flags to hinder the Templars. Both Altaïr Ibn-La'Ahad and Ezio Auditore da Firenze were known to collect them.
High Middle Ages
Flags were scattered by members of various factions throughout the Holy Land to lay claim to particular regions of territory. There were different kinds of flags, each representing a different faction. Present in each district visited by Altaïr during his hunt for the Nine, they represented the key military powers in the region. 
|Image||Flag name||Location||Number of flags|
|King Richard flags||Kingdom||100|
The Borgia also used flags to increase their control over Italy. There were 101 Borgia flags to collect in Rome. However, art merchants in the city sold maps which made it easier for Ezio Auditore da Firenze to find and remove all of the Borgia flags. An additional method to locate the flags was through Ezio's use of Eagle Vision, thus marking the flag on the map. Collecting all 101 flags rewarded Ezio with the Borgia cape. Additionally, during the Venetian games of Carnevale, the "Capture the Flag" event used a flag that Ezio had to retrieve and return to his starting point to score.
Golden Age of Piracy
During the Golden Age of Piracy, nearly all ships had a flag on the top of their mast to show an allegiance to their countries. During a boarding of an enemy vessel, Edward Kenway and Adéwalé would sometimes cut down the ship's flag upon claiming it. In 1719, Kenway was tasked with stealing a Portuguese flag, in order to disguise his ship as one of their own.
During the American Revolutionary War, after Connor killed a British Army captain and destroyed the powder reserves in one of the many forts in Boston, New York, or the Frontier, he would then take down the British flag and replace it with an American one, liberating the fort and claiming it for the Patriots.
- In Assassin's Creed, Altaïr sometimes had to prove himself to informants by collecting several Assassin flags in a certain amount of time. Upon finishing the task, Altaïr would receive information about his target.
- The Capture the Flag achievement could be earned by collecting the 101 Borgia Flags scattered around Rome.
- When taking over an Assassin-affiliated gang headquarters, the Templar Shay Cormac would cut down the gang's flag, and subsequently burn it.