On a smaller scale, units deployed aboard a starship operate under a similar, yet somewhat different, method. In addition to reporting to the regiment or battalion command in which the battalion or company serves, the Marine Commanding Officer (MCO) reports directly to the ship's captain. This instant communications and coordination allows both the naval and marine forces aboard the starship to conduct daily operations in a manner equitable to both sides. A starship-bound marine unit receives orders in much the same way. Long-term objectives are assigned by the unit's marine command while the vessel's CO is responsible for assigning short-term objectives. This has proven to be an effective method for those units assigned to serve aboard Starfleet naval vessels and installations.

Once graduated from Starfleet Marine Academy, the Marines officer is promoted to the rank of Leftenant. There is a great deal of animosity between Starfleet naval and marine officers and crew. In short, they don't get along too well. The naval complement thinks the SFMC is home to a bunch of brash, arrogant, trigger-happy folk and the marine complement believes the Starfleet navy to be lax in discipline and training. The marines also believe that the navy takes the work of the SFMC too lightly.