The structure was comparable to that of an Earth army, with similar ranks. Officers of the Militia were usually graduates of the Bajoran Military Academy, though many soldiers serving in the post-occupation period earned their rank with demonstrated skills and merit during the resistance.
The militia jointly operated Deep Space 9 with Starfleet. From 2369 to 2375 the station was commanded by a Starfleet command level officer and the executive officer was a Militia officer. When the station's commander, Captain Benjamin Sisko, disappeared in late-2375, his executive, Colonel Kira Nerys, took command.
In the non-canon novels released by Pocket Books and associated releases from WildStorm Comics, the station's new Starfleet liaison was the new XO after the events of DS9: "What You Leave Behind". First, Starfleet Commander Tiris Jast, a Bolian woman, filled the position, before dying and passing the assignment onto Commander Elias Vaughn. Following Bajor's official entry into the Federation, the station's command structure transitioned to a full starfleet compliment, with those who opted to remain in the militia rather than transferring to starfleet being reassigned to Bajor.