With the New York State Guard, as well as the Army National Guard and Air National Guard, it is under the control of the New York Division of Military and Naval Affairs and New York's Adjutant General.
The New York Naval Militia was organized as a Provisional Naval Battalion in 1889 and was formally mustered into State service as the First Battalion, Naval Reserve Artillery, on 23 June 1891. One year later the New York Naval Militia was called to active duty to protect steam ship passengers during the 1892 cholera quarantine at Fire Island.
Following the sinking of USS Maine, the Navy Department called up Naval Militia volunteers for duty in the Federal Auxiliary Naval Force. The Spanish American War had begun and the New York Naval Militia participated. New York Naval Militiamen manned two auxiliary cruisers that were engaged in the Battle of Santiago de Cuba and served aboard various other ships including patrol craft tasked with protecting New York Harbor.
During the early 1900s frequent attempts by Congress to create a National Naval Reserve failed. In 1914 however, Congress passed the Naval Militia Act which placed the State organizations under the supervision of the Navy Department.
The United States Navy Reserve was established in 1916. Only persons with prior Naval service could affiliate, leaving the Naval Militias as the only avenue for civilians to become citizen sailors. The National Defense Act of 1916 resulted in the creation of the National Naval Volunteers, which the New York Naval Militia joined en masse. The Naval Militia Marine Company was also formed in 1916. The Militia Marine Company was the first in the nation and predated the United States Marine Corps Reserve program by four months. In addition, the donation of a hydroplane marked the beginning of the Naval Reserve Aviation Program.
During the next 34 years, the New York Naval Militia (Naval volunteers/Navy and Marine Corps Reserves) were Federally mobilized for both World Wars and the Korean War. Beginning in the 1950s, many of the state militias began to disappear, but experienced a resurgence after the September 11, 2001 attacks.
At present, the New York Naval Militia has over 2,400 members, 95% of whom are also members of the U.S. Naval Reserve, U.S. Marine Corps Reserve, or U.S. Coast Guard Reserves.
The New York Naval Militia is organized into three regional commands, Southern Command, Northern Command, and Western Command; and one operational command, the Military Emergency Boat Service (MEBS).