A group of these colonists, aided by sympathetic Starfleet officers and former Bajoran Resistance fighters, formed the Maquis, which they named after a French Resistance group which fought against the Nazis during Earth's Second World War.

The Maquis had at its core several Starfleet officers who had resigned their commissions, including LCdr. Calvin "Cal" Hudson. These former Starfleet officers organised the colonists and made them an effective guerrilla force, using small warp-capable vessels aremed with surplus weapons. One of these, a modified Peregrine Class courier armed with a Type VIII phaser, was so successful that Starfleet adapted it as the Peregrine class Light Attack Craft during the Dominion War. Another, a modified Ju'Day Class light freighter, became identified with the Maquis so closely that it is still known as the Maquis Raider.

The Maquis originally confined their attacks to Cardassian shipping and military outposts, but soon began attacks on Cardassian civilians and raids on Federation outposts for supplies, and were declared an illegal organisation. Several Starfleet officers deserted to join the Maquis, Lieutenants W. Thomas Riker and Ro Laren among them, while others remained within Starfleet as "moles," like LCdr. Michael Eddington, working covertly to funnel aid and information.

The Maquis were few in number, however, and the Cardassians hunted them mercilessly. By the time Cardassia joined the Dominion and the Dominion War began, they had been virtually wiped out. Of the few who remained, many took advantage of a Federation amnesty and joined Starfleet in fighting the War, while others aided the new Bajoran Resistance when the Dominion occupied Bajor.

The Maquis as it was no longer exists, but two groups claim the name. One is a lobby group made up of former colonists who are fighting a legal battle for reparations, The other is a loose collection of Starfleet deserters and hangers-on who have gone renegade, conducting sporadic raids on Cardassian planets as well as indulging in the odd act of piracy on Federation, Klingon and other trading vessels. The Renegade Maquis, or Maquis Forces (as they call themselves) are based on Empok Nor, another abandoned Cardassian station.