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Although under the authority of the Commandant of the U.S. Coast Guard, the Auxiliary is autonomous, operating on four organizational levels: Flotilla, Division, District Regions and National.
- Flotilla - The flotilla is the basic organizational unit of the Auxiliary and is comprised of at least 15 qualified members who carry out Auxiliary program activities. Every auxiliarist is a member of a local flotilla. Each flotilla is headed by a Flotilla Commander (FC).
- Division - For maximum administrative effectiveness in carrying out Auxiliary programs, flotillas in the same general geographic area are grouped into divisions. The division provides administrative, training and supervisory support to flotillas and promotes district policy. Each division is headed by a Division Commander (DCDR), and Division Vice Commander (VCDR), and usually consists of five or more flotillas.
- District/Region - Flotillas and divisions are organized in districts comparable to the Coast Guard Districts. Some districts are further divided into regions. The district/region provides administrative and supervisory support to divisions, and promotes the policies of both the District Commander and national Auxiliary committee. All districts and regions are governed by a District Commodore (DCO), District Chief of Staff (DCOS), and District Captains (DCAPTs), under the guidance of the Coast Guard District Commander. At this level, Coast Guard officers are assigned to oversee and promote the Auxiliary programs as district Directors of Auxiliary (DIRAUX).
- National - The Auxiliary has national officers who are responsible, along with the Commandant, for the administration and policy-making for the entire Auxiliary. These officers comprise the National Executive Committee (NEXCOM) which is composed of the Chief Director of Auxiliary (an Active Duty officer), National Commodore and the National Vice Commodores.